Qingyuan County, Zhejiang, China is recognized as a source of mushrooms around the world and as Mushroom City in China. Because of a favorable ecological environment and abundant forest resources, mushroom farmers in Qingyuan have engaged in mushroom production for 800 years and continued to form unique mushroom production systems where people and nature live in a harmonious way, and a rich and colorful mushroom culture. The Qingyuan Mushroom Culture System was named the Nationally Important Agricultural Heritage systems of China in 2014. Based on analysis of the importance of agricultural heritage and the necessity and urgency of protection, here we examine the agricultural heritage of the Qingyuan mushroom culture system as a research case study and comprehensively describe its heritage values, including supply materials and production, ecosystem services, cultural inheritance and multi-function agricultural development. These results provide reference values for agricultural heritage protection and inheritance of edible fungi in China, agricultural sustainable development and extension of agricultural function.