The ecological value encapsulated in the term “spiritual ecology” is drawing more and more attention from ethnology, folklore, ecology, and other related disciplines. The custom of respecting and pacifying forest spirits has distinct regional and ethnic characteristics, and many scholars have discovered samples from different studies around the world. Qingyuan County, located in the mountainous region of southwest Zhejiang, is a very typical case of the practice of respecting and pacifying forest spirits. The mushroom-cultivation technology invented by the chthonic people there more than 900 years ago made this the global birthplace of artificial mushroom cultivation. The Qingyuan Forest–Mushroom Co-cultivation System (QFMCS) has been listed as an important agricultural heritage system by the Ministry of Agriculture and Rural Affairs of China, Beijing, China and a candidate project by the Food and Agriculture Organization of the United Nations, Rome, Italy for Globally Important Agricultural Heritage Systems (GIAHS). Additionally, the QFMCS is currently an important part of the Baishanzu National Park under construction. The authors made an in-depth field study in the mountainous areas of Qingyuan and used theoretical methods of ecology, anthropology, and folklore to reveal the function spiritual ecology plays in ecological conservation, forest protection, identity, and the maintenance of community interests. In the “traditional-modern” transformation of Qingyuan County, the practice of respecting and pacifying the Spirits is still being propagated, resulting in expansion and social cohesion.