Centre-back Flint, 27, who has made 169 appearances for the Robins and scored 25 times, will now stay at Ashton Gate until the summer of 2020.
Bristol City boss Lee Johnson said: “Aden’s career progression has been excellent, right through from his non-league days.
“He’s continued to impress for us, gaining experience at Sky Bet 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 said: “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.”