Chairman Stephen Murphy will assume Marshall's responsibilities until a successor is appointed, the company said in a statement.
He said: "The Board would like to thank Nicholas for his significant contribution to the company.
Under Nicholas' leadership over the last four years, The Garden Centre Group has established itself as the garden centre market leader in the UK with a high quality horticultural offering in 129 garden centres across England and Wales. It has also expanded its restaurant and concession businesses to be major contributors across the estate."
GCG was bought by private equity firm Terra Firma in March this year.
Its chairman Guy Hands said: "Terra Firma thanks Nicholas for having done an outstanding job at stabilising the business over recent years and focusing its core business on providing first class products to Britain's gardeners. We look forward to working with Stephen Murphy as he builds on the strong platform for growth that Nicholas leaves behind."
Nicholas Marshall said: "I would like to thank everyone in The Garden Centre Group for their unceasing hard work and loyalty over the last four years. They should all be very proud of their achievement".
The board has begun a search for a new chief executive.