The 27-year-old joined the Robins in 2013 and was an integral part of the side that claimed the League One title in 2015, with 14 goals in 46 appearances.
"Aden's career progression has been excellent, right through from his non-league days," said head coach Lee Johnson. "He's continued to impress for us, gaining experience at Championship level. His attributes are clear for everyone to see; his physical presence as well as his defensive and goalscoring abilities.
"He's valuable for us and we felt it was the right time for us to invite him in and talk about an extended deal, which we're delighted he has signed."
Flint added: "It was an easy decision for me. I've been here for four years now; it was a tough start but I haven't looked back since.
"I've already got a lot of happy memories and hopefully there will be plenty more. Bristol City feels like a family. We're a tight-knit group and I couldn't be happier to agree a new contract here."
Bristol are currently 13th in the Championship, five points off the playoff places.