He says he wants the Hammers to win their final game at Upton Park, but does not expect them to do so.
Merson had previously said he believed West Ham would win their final three games of the season, but feels let down by the team's 4-1 loss to Swansea City at the weekend, suggesting the team were over confident.
He said: "It looked like they turned up against a Swansea side - who made six changes - thinking they would win.
"It pains me to say it but I think Manchester United are going to win and keep the race for the top four in their hands. No disrespect to Manchester United but I don't want to see West Ham lose their final game at the Boleyn Ground."
Merson went onto predict Louis van Gaal's side will win 2-1 on Tuesday night.
The Swansea result could work against Manchester United, and ensure West Ham are more up for this game than ever to ensure there is not a repeat, and make it up to their supporters.
United have already won once this season at West Ham, beating them 2-1 in the FA Cup, with striker Marcus Rashford making a big impact.