To understand the relationship between soil fauna and microorganism in the detrital food chain during litter decomposition, leaf litters of poplar (Populus simonii) and fargesia (Fargesia spathacea) in a subalpine forest of western Sichuan were taken as study objects. Phospholipid fatty acid (PLFAs) biomarker method was used to determine the effects of soil fauna on the abundance, structure and diversity of microbial community during the decomposition of leaf litter of two species from April 2016 to April 2018 with in situ control experiment. The results showed that the presence of soil fauna significantly affected the microbial PLFAs content during the decomposition of both species, reducing the PLFAs content in the first 240 days and increasing the PLFAs content in the 360 to 480 days. Soil fauna participation reduced the ratio of fungi to bacteria in the decomposition of poplar litter, and increased the ratio of gram-positive bacteria (G) to gram-negative bacteria (G), which had the opposite effect on the ratio of fungi/bacteria and G/G in the decomposition of fargesia litter. Microbial diversity and evenness maintained a high level in 120 and 480 days of the decomposition, and decreased sharply in 360 and 720 days of decomposition. Soil fauna participation significantly affected microbial diversity and evenness of poplar litter, but it had no signifi-cant effect on fargesia litter. The effects of soil fauna on the changes of litter PLFAs content were different with the decomposition days and tree species. The interaction between soil fauna and microbial community during litter decomposition in subalpine forest varied with seasons and tree species.