Appointed in May 2010, when the club were in the Evostik League, the 39-year-old steered the Chester to unprecedented success, guiding them to three successive league titles and back into non-league’s elite.
But this season has presented unfamiliar difficulties and, with Chester battling relegation, Young told The Chester Chronicle the time was right to move on.
“I love a cliche and all good things must come to an end at some time,” he said.
“I’m very proud to have been given the opportunity to manage such a fantastic club and the memories of the last three years will live with me forever.”
“To start a club with nothing and three years later be in the Conference Premier, to break so many records and win so many awards has been amazing,” he said.
“I have had some fantastic times and it’s a massive credit to everybody involved to have got the club to where it is today.
“We have been on an amazing journey together. If we could go back in time and do it all again then I’m sure that we would.”
Young plans to take a break from the game and spend more time with his wife and two young daughters.
“From the start I have put so much time into Chester and I am grateful to my family for allowing me to do that,” he said.
“It’s the first time in 14 years I have been out of football and I have made a lot of sacrifices and my kids have got their dad back now.”
Young’s best friend Gary Jones steps up from his role as assistant manager to become caretaker boss as the club begins the search for his successor with Saturday the deadline for applications.
Possible contenders include sacked Kidderminster Harriers boss Steve Burr and ex-Luton Town manager Gary Brabin.
Airbus UK boss Andy Preece and former Chester City defender Iain Jenkins, now working for the Scottish FA, could also be keen.
“The players are going to need the fans behind them more than ever and so is the new gaffer," said Young.
“I hope I always have a fantastic relationship with the supporters and I’m very proud I can walk away from the club with this legacy.”