The 19-year-old Welshman, who scored three times in 12 appearances as he broke into the side last season, will stay with the club until 2016.
"I am delighted we have got a young player of Ellis' ability to stay with the club for this length of time," manager John Ward told the Bristol Evening Post.
"Hopefully, he and the club can develop together and achieve some success.
"Over the next couple of years we expect more games for him, and for him to develop at Football League level.
"We have already seen what he is capable of, but he is only 19 and there needs to be patience from Ellis, myself and the supporters. We have a great opportunity here."