The 20-year-old, who scored one goal in 35 appearances last season, is set to sign for another club this week.
Shrimps manager Jim Bentley told the club website: "We made Jordan an offer but again it was on reduced terms and he has decided not to accept.
"I'm really sorry to see Jordan leave because I really do think he has a bright future in the game.
"He has a lot of strengths and is getting better all the time, but he sees his future elsewhere and I hope he does really well for himself.
"I know a couple of other Football League clubs have been looking at him and I am sure he will get another club soon."
Nick Fenton, Will Haining and Gary McDonald have also left Morecambe since the end of the season.