Downed logs are important structural and functional elements in the material flow of global forest ecosystems. They provide a rich natural substrate resource for microorganisms; however, current laboratory-based methods cannot fully elucidate the complex process of microbial decomposition of downed logs. Therefore, our study investigated the microbial community structure, succession patterns, and underlying environmental factors controlling the decomposition of Pinus tabulaeformis and Quercus aliena var. acuteserrata downed logs at different stages of decomposition in Chinese forest ecosystems. The genomes of the microorganisms present on the logs during different stages were therefore sequenced, and functional genes were annotated and analyzed using the Kyoto Encyclopedia of Genes and Genomes and Carbohydrate-Active enZYmes databases. We found that bacterial abundance was always higher than fungal abundance throughout the decomposition process, reflecting their strong competitive ability. Microbial community structure and function were similar in the early stage (I) and late stages (IV, V) of log decomposition, but those of the middle stages (II, III) differed. With the decomposition of downed logs of Q. aliena var. acuteserrata, there was a fungal succession pattern from Ascomycota to Basidiomycota to Mucoromycetes, but this trend did not occur for P. tabulaeformis. The density, moisture and elemental content of downed logs were the main factors affecting the microbial community. Finally, microbially mediated functions were mainly related to the metabolism of amino acids, carbohydrates and various small molecule carbohydrate enzymes, cellulases, and chitinases in glycoside hydrolases; the taxa sources of the main functions were primarily Proteobacteria and Firmicutes bacteria, reflecting the functional importance of bacteria in the process of downed log decomposition. We conclude that bacteria always play an important role in the process of downed log decomposition and that their role may be far underestimated. Therefore, we believe that the next step should be to expand the study of downed log bacteria, to further clarify the ecological functions of the bacteria on downed logs in natural environments and their relationship with fungi, which may help shed light on the complex decomposition process of downed logs.