Cordyceps militaris (CM) is widely distributed in humid temperate and tropical forests. Commercially available CM is mainly dried fruiting bodies and their further processed products. In the Chinese market, these products are mainly stored at room temperature without vacuum sealing after air drying. In this study, ultra-high performance liquid chromatography-high-resolution mass spectrometry, gas chromatography-mass spectrometry, and microbial community abundance analysis were applied to analyze the changes of major metabolites and microbial communities in CM dried products and explore the changes in quality during storage at room temperature. A total of 856 non-volatile and 431 volatile substances were detected, of which 195 non-volatile and 85 volatile substances showed significant differences. By analyzing the microbial community relative abundance, the highest relative abundance was observed in the second month, which was then followed by a decline. These results demonstrated that the quality, odor, and nutrient content of CM changed considerably after storage from one to two months. These findings can provide new insights for exploring the optimal consumption time for the best flavor and health function of CM dried products in the future.