Sixty-four clubs will take part in the competition, formerly known as the Johnstone’s Paint Trophy, starting in a group stage.
The 16 groups will be made up of at least one club from each of Leagues One and Two, along with one invited team.
The top two sides in each group will then go into a knockout stage with the final played at Wembley on 2nd April.
Clubs invited to enter their Under 21 sides are Arsenal, Chelsea, Everton, Leicester City, Liverpool, Manchester City, Manchester United, Middlesbrough, Newcastle United, Southampton, Stoke City, Sunderland, Swansea City, Tottenham Hotspur, West Bromwich Albion and West Ham United.
Football League clubs will have to field at least five ‘first team’ players in their EFL Trophy starting line-ups, while only six of the players in the invited clubs’ starting 11 must be under the age of 21.
In the group stages clubs will play each other once, either home or away, while the invited clubs will play one of their home games at the club’s first team stadium.
Clubs will be awarded three points for a win and one for a draw, but in the event of a drawn game after 90 minutes, a penalty shootout will be held to award an additional point.
In round two the draw will remain regionalised with group winners drawn at home to a second placed team from a different group.
Rounds three and four will be ‘free’ draws.
EFL chief executive, Shaun Harvey said: “The new format is intended to rejuvenate this competition and also assist the development of the very best young players in English football. This will help us deliver more and better home grown players which will deliver benefits to the national team and domestic league football at all levels.
“I believe this is the right time to pilot these changes to the EFL Trophy, which we will review at the end of the 2016/17 season following discussions with our clubs and having consulted with the other football bodies and supporter organisations.”
A Premier League spokesman added: “The overriding aim of the Elite Player Performance Plan across the Premier League and English Football League is to produce more and better home grown players capable of performing at first team and international levels.
“Participation for a selection of Premier League clubs’ teams to take part in the EFL Trophy is an important part of a range developments that both we and the EFL believe will help young, talented players progress physically and mentally on top of the technical aspect of their game developed in the Academy system.
“It is a progressive move by both leagues; one that we welcome.”
The group stage games will be played on the weeks commencing 29th August, 3rd October and 7th November.
No date has yet been announced for the initial group draw