Lentinula edodes (L. edodes) is a premium edible fungus cultivated extensively throughout China, and Lyophyllum decastes (L. decastes) is a wild edible fungus with a high degree of industrial-level cultivation in China. Regarding the edible value of the two fungi, research on their medicinal properties is relatively scarce. In this study, we utilized ultra-high performance liquid chromatography with quadrupole and time-of-flight mass spectrometry to analyze comprehensively the chemical composition of both fungi. In all, 120 and 144 chemical components were identified in L. edodes and L. decastes, respectively. Subsequently, we elaborated active components, potential biological activities, and therapeutic targets associated with both fungi by using network pharmacology. The results showed that seven active components in L. edodes and nine active components in L. decastes could act on common targets, such as AKT serine/threonine kinase1 and peroxisome proliferator-activated receptor gamma, thereby regulating signaling pathways, such as epidermal growth factor receptor and mitogen-activated protein kinase, to affect the body. In addition, these components affect immune regulation and inhibition of liver cancer. Finally, we used cell experiments to verify their activities. Our findings provided a reliable foundation for future research aimed at harnessing the bioactivities of L. edodes and L. decastes, thereby offering novel strategies for their utilization in the field of functional foods and natural medicine.