The Red Devils have taken two points from their opening three Premier League games, and have used the 3-5-2 formation in all their matches, despite players looking uncomfortable in the system.
"If Van Gaal is determined to persist with a back three this is going to be a long and painful transition," Souness wrote in The Times.
"Robin van Persie... doesn't look right [and] there is a question mark over Radamel Falcao as well. In taking him from Monaco and selling Danny Welbeck, United again seem to be moving away from what they have always been about."
United face Queens Park Rangers in their next Premier League clash on Sunday.