The 20-year-old midfielder will now remain with the Sky Blues until summer 2016.
Manager Steven Pressley told the club's official website: "Conor is a blueprint for the kind of young players we want to develop at this club.
"He's extremely talented, he's dedicated and he has a very bright future as he's shown in the way he has performed for us this season.
"He works just as hard off the pitch as he does on it and he's a fine example to other young players hoping to progress through the club's ranks. I'm delighted he has committed his future to us."
Thomas has made 20 appearances in all competitions for Coventry so far this season.