In what will be a one-season trial, 16 tier one academy teams - most of which are in the top flight - will join the competition, formerly known as the Johnstone's Paint Trophy, alongside League One and League Two teams.
In a statement on the official Notts website, a statement said: "The discussion at the EFL Conference confirmed the competition is in serious need of innovation to survive and a number of clubs even stated they would consider withdrawing from the competition if it was not boosted.
"Many clubs struggle to break even from EFL Trophy matches, and numerous clubs voiced genuine concerns the competition would fold if it does not improve quickly, as the prize money and TV interest is low.
"Notts County supported the decision to trial a solution to save the competition, which currently does not have a sponsor. This is for a set period of one year and if the proposals do not work, they will not be renewed for the following season. The prize money for the competition will be doubled for next season.
"This is not in any way opening the door to Premier League 'B Teams' entering the league structure and Notts County would be vehemently against any such proposals.
"While some supporters will disagree with the proposed changes, after careful consideration and discussion, we felt that it was important to explore ways to boost the competition and ensure that it could continue."
The changes, which include the introduction of a group stage, were voted for by more than 50 percent of clubs in the bottom two tiers of the Football League and will see the Premier League increase the prize fund by £1m.