Youth team manager Tony Philliskirk believes next season will be tough for his youngsters as the league has extended from 23 games to 30.
Latics will be in the North West division with teams such as Bury, Rochdale and Preston North End.
The restructuring of the league means Latics will have to play an extra seven games in the league along with cup games and Philliskirk admits it could be tough for his players.
He said: "It will make a massive difference. It will be a pretty cramped fixture list and put that with the cup games, it's going to be a tough schedule for the lads this year.
"We are really going to have to structure the coaching plan this year based around the extra fixtures."
With the Youth Alliance league set to start on August 2, preparations have been further hampered which the manager explains: "What makes things worse is that we are in Holland for the first two fixtures so we will have to reschedule those.
"The lads will want to play games but at the start of the season we will be playing catch up. There isn't much rest for the lads this season, not like last," continued Philliskirk.
"Everybody wants to play games but it could go either way with how the players react. We'll need all 18/19 players that I have this year. It's going to need a lot more organisation from us to accommodate the increase in games next season."
After the success of last season's Lancashire FA Youth Cup victory, the manager is looking for the players to kick on and look to win the league this season.
"We did ever so well last year but we had a lot of injury problems so the first years really excelled. There might be a little expectation of them this season because they did so well last season. It will be interesting to see how they mentally adapt to that."