Budgetary restraints at the Globe Arena forced the Shrimps to part company with Nick Fenton earlier this month and fellow centre-back Haining must leave in similar circumstances.
Saturday's 1-0 win at Southend will stand as the 30-year-old's 133rd and final appearance for Morecambe, who he joined in summer 2009 after being released by St Mirren.
"It's a similar story to Nick Fenton really," Morecambe boss Jim Bentley told his club's official website.
"We wanted to keep Will and he wanted to stay but we could only offer reduced terms and couldn't agree a deal to keep him here at this moment in time.
"It's another disappointment for us as he showed (against Southend) just what a good player he is but we know what we have to work with next season and that has to be the way forward.
"I would like to thank Will for everything he has done for us. He has been a great lad to have around and we wish him well for the future."
Bentley added: "We have said all along there may be some senior players leaving because of the wage structure but that is where we are as a club and we are now ready for the challenge of bringing in new players for next season.
"We are watching a lot of games at the moment and are planning for a busy summer to bring the best players we can to the Globe."