Jones was born and brought up in Bournville in the south side of Birmingham, England. Her mother worked in advertising and her father was a journalist. Her uncle is an actor, which prompted Jones' interest in acting as a child. One of her great-great-grandmothers was Italian, from Lucca, Tuscany.
She studied English at Wadham College, Oxford. She appeared in student plays, including Attis in which she played the title role, and, in 2005, Shakespeare's The Comedy of Errors for the Oxford University Dramatic Society summer tour to Japan, starring alongside Harry Lloyd.
Jones began acting at the age of 11 at after-school workshop Central Junior Television funded by Central Television. She appeared in the first series of The Worst Witch. When Weirdsister College began in 2001, Jones returned as Hallow. Her longest and best known role around this time was on the BBC Radio 4 soap opera The Archers, where she played Emma Carter until 2009 (currently played by Emerald O'Hanrahan).
In 2003, she starred as Grace May in the BBC drama Servants. She took the leading role in the 2007 ITV adaptation of Jane Austen's Northanger Abbey, and made her stage debut in Polly Stenham's That Face at the Royal Court Theatre in April 2007.
In 2008, she appeared in the films Brideshead Revisited and Flashbacks of a Fool, the Doctor Who episode "The Unicorn and the Wasp" and a revival of Enid Bagnold's The Chalk Garden at the Donmar Warehouse theatre in London. In January 2009, the five-part TV serial The Diary of Anne Frank, in which Jones played the role of Margot Frank alongside Tamsin Greig (as Edith Frank-Holländer) and Iain Glen (as Otto Frank), was broadcast on BBC One. Later that year in May, she performed in a rehearsed reading of Anthony Minghella's Hang Up at the High Tide Festival. Jones played the role of Julie in Ricky Gervais and Stephen Merchant's 2010 film Cemetery Junction. She also appeared in Soulboy and in Julie Taymor's big screen adaptation of The Tempest as Miranda.
On 29 January 2011, Jones won a Special Jury Prize (Dramatic) at the Sundance Film Festival for her performance as Anna in Drake Doremus's Like Crazy. She had to do her own hair and make-up in the film, while the dialogue was entirely improvised. Her performance earned comparisons to Carey Mulligan's Academy Award-nominated role in An Education. She also received the Best New Hollywood Award for this film at the 2011 Hollywood Film Awards. She appeared alongside Gossip Girl actor Ed Westwick in Chalet Girl, a romantic comedy released in March 2011, for which she had to undergo two months of snowboarding training and work undercover in a chalet at St Anton, scrubbing toilets and partying at the Krazy Kanguruh bar in preparation for the role. Jones said that the role was "something of a relief" after a string of costume roles and she was also keen to take on a comic role. Jones performed in Luise Miller, a new translation of Schiller's Kabale und Liebe by Mike Poulton at the Donmar Warehouse theatre in London, in June and July 2011. Jones lived with a Catholic family and attended Mass to prepare for the role. In 2011, Jones was announced as the new face of Burberry. In November, she was also announced as the new face of Dolce & Gabbana.
In 2013, Jones portrayed Ellen Ternan in The Invisible Woman. Jones, previously unfamiliar with Ternan for the most part, learned about her life through research, and reflected that she knew she was "in for a challenge" when choosing to work on the film, citing the experience of director Ralph Fiennes and how "methodically done" his performance was. She also co-starred in The Amazing Spider-Man 2, which was released on 2 May 2014. She played Felicia Hardy; an assistant of Harry Osborn. Jones signed on due to its difference from her previous works.
In 2014, Jones portrayed Jane Wilde Hawking in the film The Theory of Everything, a biopic charting the life and love between Wilde Hawking and the world-renowned physicist Stephen Hawking, with Eddie Redmayne starring as Hawking. After being given the script by her agent, Jones read it in its entirety in one sitting, enjoying that it was a "love story and not a straightforward biopic." She auditioned for the film and its director, James Marsh, offered the part immediately after, surprising Jones who was accustomed to waiting several weeks for a confirmation. Jones was aided by Jane Hawking in preparing for the role, meeting with her. The film has been praised largely due to her and Redmayne's performances. Jane Hawking was so impressed by the portrayal she wondered if it was herself when watching Jones. For her role as Jane, she received widespread acclaim from a number of organizations, including nominations for an Academy Award for Best Actress, a BAFTA Award for Best Actress in a Leading Role, a Golden Globe Award for Best Actress, a Critics' Choice Movie Award for Best Actress and a Screen Actors Guild Award for Outstanding Performance by a Female Actor in a Leading Role.
In February 2015, she was cast as Jyn Erso in the Star Wars stand-alone film Rogue One, with Gareth Edwards directing. Jones's agent recommended the role to her, and she enjoyed the character's search for an identity, drawing inspiration in her movements from Ronda Rousey. The film was released in December 2016 to positive reviews and grossed over $1 billion at the box office. Also in 2016, Jones starred in Inferno, playing a doctor aiding Robert Langdon in his escape. According to director Ron Howard, Jones' only reluctance to signing for the film was the ensuring of her having days off to see the birth of her brother's child. After agreeing to the role, she visited museums and galleries to better understand her character. Jones enjoyed the chemistry between her and Tom Hanks's characters as well as Inferno's overall diversity.
In 2013, Jones split from her boyfriend of ten years, sculptor and Internet artist Ed Fornieles, whom she had met at Oxford when he was at the Ruskin School of Art. In 2015, she began dating director Charles Guard. Their engagement was announced in May 2017.
Jones identifies as a feminist.