Young has led the Mariners to the third round of the FA Cup, where they will host Premier League giants Tottenham Hotspur on January 10 in what will be the biggest gap between two competing teams in history.
Their record-breaking run has taken in seven victorious rounds so far, including beating Football League side Colchester United.
Young said: “I’m very proud to be the Manager here. I would like to thank the club for showing their faith in myself and my staff and believing in what we are working towards to drive the club forward.
“It’s been a tough number of years for our supporters but I must say in the time I have been here they have always stuck with the players and I have been amazed at their support.
“This cup run is a thank you to them for their continued unwavering support and I intend it to be, only the start of this new chapter.”
Marine were relegated for the first time in their history in 2019, and last year celebrated their 125th anniversary.
They were third in the NPL N/West Division table when the season came to a halt back in March, and have won four of their six league games in 2020/21 so far.
Club chairman Paul Leary added: “This is really great news for everyone at Marine Football Club. Our team, with Neil at the helm, has created history with the Emirates FA Cup run and this announcement of a 3 year+ agreement is well deserved and could not be timed better.
“The agreement with Neil paves the way for him to build on this year’s amazing achievements and to continue to plan and achieve improvement especially in league standings.”
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