Paynter formed an impressive strike partnership with 32-goal Simon Cox over the course of the season, chipping in with 12 goals of his own.
And Wilson hopes the introduction of new faces in attack next season will spur the former Port Vale man on to greater heights.
The manager told Swindon's official website: "Billy was the unsung hero last season.
"Coxy got a lot of recognition and rightly so with the amount of goals he got but I'm delighted Billy finished the season the way he did.
"Any player under competition should be spurred on to better things and I'm sure Billy will be looking forward to seeing who we bring in."