The invention relates to a method for biologically converting cotton by-products into glossy ganoderma, which comprises the following steps: (1) pulverizing wizened cotton stalks or soaking integral cotton stalks in water; (2) preparing a culture medium and treating materials; (3) disinfecting, sterilizing and inoculating; (4) culturing mycelia; (5) building a greenhouse, and putting the mycelia into soil for culturing; (6) regulating and controlling temperature, illumination, moisture and humidity; (7) opening the bag of the mycelia, and reserving and controlling growing points; (8) preventing and treating diseases and pests; and (9) harvesting fruit bodies and spore powder. The method uses by-products, including cotton stalks, cotton branches and cotton seed hulls, in the production of cotton as base materials for culturing glossy ganoderma to replace traditional basswood raw materials, which not only improves the utilization ratio of agricultural resources and the production efficiency of industries but also develops a novel resource for the edible fungus industry, thereby reducing forest destruction, protecting forest resources, solving the contradiction between the development of the edible fungus industry and the supply and demand of resources, and solving the contradiction between the development of the edible fungus industry and the forest ecological protection. The method can effectively utilize, save and increase resources, has wide adaptability and is favorable for promoting the development of agricultural circulation economy.