The 18-year-old, who signed his first professional contract with the Rams in 2012, is regarded as of the brightest youngsters in England.
His performances this season have reportedly drawn interest from Barcelona, but Clough has refused to comment on the transfer speculation.
"He's had a great season and we really do believe he'll be even better next year," Clough told the club's official website.
"Will has shown he has plenty of potential this season and if continues to keep his feet on the ground and concentrate on his football, he can be anything he wants to be.
"A year ago he hadn't even started a game, but he's gone on to make over 30 starts this year, score a few goals and get capped by England at Under-21 level. So when you look at it that way, he's had an amazing year."
Hughes joined the club in 2006.