The invention relates to a method and a device for culturing native mushrooms. Primarily, culture media contained strains are disposed in a container. Filter materials with laminated and dense holes are covered on the top of the culture media. Thereby filter materials with laminated and dense holes are utilized to replace covering soil for supporting the growth of the native mushrooms. Thus, it can avoid that hazardous substances such as heavy metals contained in the covering soil are absorbed by mycelia of native mushrooms during the growth procedure of the native mushrooms. Accordingly, it can achieve the substantial effects of ensuring the food safety of native mushrooms.