The experienced manager helped preserve the club’s National League North status, achieving his remit of keeping the side in the division following promotion last May.
Now he is to become the club’s first ever Director of Football at the end of the current season.
It is a role that will see him "lead all football operations, shaping the club’s sporting strategy to drive success for the men’s first team".
He has been in the job for almost seven years and Young says he hoped the day he would leave the dug-out would never come.
“It’s obviously very difficult to step away from my role as manager, but I know personally now is the right time for me, but more importantly for the football club," he told the club's website.
“The last two years have been very demanding from a manager’s perspective with promotion last season and the importance of keeping Marine at National League North level this year.
“I am so happy we had the opportunities to experience and create so many memories that will last a lifetime.
“It was very important for me after everything that has been achieved and all the relationships and friendships that we have built over the many years that I left through the front door with an opportunity in our last three games to say thank you to everyone.”
He went on: “I’m really looking forward to my new role as Director of Football, it’s an important development for the club and key to modernising our structure in the current game.
“The next phase of the club’s development will show ambition and will allow the new manager to concentrate solely on his role with a support network around him to help him push the club forward and ultimately bring success.”
Marine CEO James Leary is excited for the future - but knows they’re losing a great manager.
“Neil has done an incredible job over the last 6+ years,” he said. “He has created memories for every Mariner that will stay with us forever and has completely transformed Marine Football Club as we knew it.
“It is an incredibly sad day that this era has now come to an end. The 6+ years have been incredibly intense, and I know that Neil has devoted everything he has got to making Marine successful.
“Following conversations with Neil we recognised that this could be an opportunity to accelerate a restructure of the football side of the club to allow us to professionalise and compete more effectively going forward.
“I am delighted therefore that as part of the changes, Neil is to take on the newly formed role of Director of Football. This will give us consistency and stability following the years of success we have enjoyed whilst putting into place the restructure we feel is needed.”