Jones was born in Bromley, London, the only child from the marriage of David Bowie and his first wife, Angela, a Cypriot-born American former model. His birth prompted Bowie to write the songs "Kooks" and "Oh! You Pretty Things" for his 1971 album Hunky Dory.
Jones spent time growing up in London, Berlin, and Vevey, Switzerland, where he attended the first and second grade at the Commonwealth American School (now the International School of Lausanne) in Lausanne. When the Bowies divorced in February 1980, David Bowie was granted custody of nine-year-old Jones (who was then known as "Zowie"), and he visited his mother on his school holidays until ending contact with her at age 13. They remain estranged. At age 14, he enrolled in the Scottish boarding school Gordonstoun.
At the age of 12, Zowie decided that he preferred to be called "Joey", and used this nickname until shortening it to "Joe" in his later teen years. The press reported that he went by "Joe" in 1992 when attending his father's wedding to Iman. At this wedding he was the best man. Whilst growing up, Jones dreamed of becoming a professional wrestler, and his father frequently praised what he called Jones' "natural strength." He reverted to his birth name around the age of 18.
By 1995, Jones graduated with a bachelor's degree in philosophy from the College of Wooster. He then pursued a Ph.D degree at Vanderbilt University in Tennessee, but left before completion to attend London Film School, where he then graduated as a director in 2001.
Jones was one of many cameramen at his father's widely televised 50th birthday party directed by Englishman Tim Pope at Madison Square Garden in 1997 and also at two BowieNet concerts at Roseland Ballroom in New York City in June 2000. He was also the in-game cinematics director for the political simulator Republic: The Revolution, as well as scripting elements of the game.
Jones directed the 2006 campaign for the French Connection fashion label. The concept of 'Fashion vs Style' was to re-invigorate the brand and move it away from the former incarnation of FCUK, which style pundits believed had become tired and overused. The advert debuted in the week ending 20 February 2006 and featured two women (representing fashion and style) fighting and briefly kissing each other. The advertisement generated 127 complaints to the Advertising Standards Authority.
Jones's first feature film, Moon, was nominated for seven British Independent Film Awards in 2009, and won two, Best British Independent Film, and the Douglas Hickox Award for Best British Director on their debut feature. It was also nominated for two BAFTA Awards at the 2010 ceremony, winning Jones the BAFTA Award for Outstanding Debut by a British Writer, Director or Producer. There have been 19 other nominations and wins for the film, from film festivals and societies, including the BAFTA Carl Foreman Award.
He directed the Summit Entertainment project Source Code, a science-fiction thriller from Vendome Pictures, which was produced by Mark Gordon. Source Code was released on DVD and Blu-ray on 26 July 2011 in the United States.
On 30 January 2013, Jones was announced to direct the Warcraft film adaptation, which was released in the summer of 2016. In November 2015, Jones announced his next film after Warcraft will be the science fiction thriller Mute, starring Alexander Skarsgard and Paul Rudd. Jones had been developing the project for years and described it as a "spiritual sequel" to Moon, inspired by Ridley Scott's Blade Runner. The film, set in Berlin forty years in the future, will follow a mute bartender investigating his partner's disappearance. Jones announced on his Twitter that filming would begin on 28 September 2016. Liberty Films UK confirmed that principal photography had begun that day.
Jones announced his engagement to photographer Rodene Ronquillo on 28 June 2012. They married on 6 November 2012. On the same day, Ronquillo was diagnosed with breast cancer. The couple have been campaigning to raise awareness for the disease and for early diagnosis since then. In February 2016, Jones and Ronquillo announced on Twitter that they were expecting their first child, due that June. On 10 July 2016, Ronquillo gave birth to their son Stenton David Jones. Jones announced his birth on 29 July 2016.
Jones is the half-brother of Alexandria "Lexi" Jones (born 2000), the daughter of his father and his father's second wife, the fashion model Iman. He is also the half-brother of Stacia Larranna Celeste Lipka (born 1980) from his mother's relationship with musician Drew Blood (real name Andrew Lipka). He has a stepsister, Zulekha Haywood (born 1978), who is the daughter of Iman and former NBA basketball player Spencer Haywood, Iman's second husband.