Young`s management team of Gary Jones, Alex Hay and Carl Garner have also left Edgeley Park.
Young said: "I've worked tirelessly since arriving at the club towards the end of May and although after a good start, recent results have not been good enough, I do believe on numerous occasions misfortune has played its part.
"I have another full-time job and a young family and after those recent results and in particular Saturday's it has really taken its toll, so I've decided to step down with immediate effect.
“I am extremely proud to have been able to manage two of the biggest clubs in non-League football in my managerial career and may now look at a different role within football. I believe I am leaving Stockport County with a strong squad of players and in a better place off the field.
"I would like to thank all of my players, my staff whose commitment to me has been unbelievable and the very kind people who work very hard within the football club for their generosity towards me. Finally, I would like to wish all our supporters and everybody at the football club all the very best for the future."
The Board of Directors plan to announce Young's replacement shortly.