• Decay stages and meteorological factors affect leaf litter’s microbial community.• Bacteria and fungi were mainly affected by OC, TN, pH, and water content of leaf litter.• Bacterial (6.6) and fungal (3.6) Shannon indexes were the largest after 125 days.• Microbial diversity and decay stage directly regulated the litter mass-loss rate.Litter microorganisms play a crucial role in the biological decomposition in forest ecosystems; however, the coupling effect of meteorological and substrate changes on it during the different stages of leaf decomposition in situ remains unclear. Hence, according to meteorological factors dynamics, a one-year field litter of Quercus wutaishanica in situ decomposition experiment was designed for four decay stages in a warm temperate forest. Microbial community composition was characterized using Illumina sequencing of fungal ITS and bacterial 16S genes. Bacterial (6.6) and fungal (3.6) Shannon indexes were the largest after 125 days’ litter decomposition (October). The relative abundance of Acidobacteria after 342 days and Bacteroidetes after 125 days were 3 and 24 times higher than after 31 days, respectively. Some non-dominant species (bacteria: Firmicutes, Planctomycotes, and Verrucomicrobia; fungi: Chytridiomycota and Glomeromomycota) may be absent or present at different decomposition stages due to litter properties or meteorological factors. Chemoheterotrophy and aerobic-chemoheterotrophy were the dominant bacterial functional groups, and the dominant fungal functional groups were saprotrophs, pathotrophs, and symbiotrophs. Precipitation and relative humidity significantly affected bacteria. Temperature, sunlight intensity, and net radiation significantly affected fungi. Besides, among the relative contributions of changes in bacterial and fungal community structure, leaf litter properties alone explained the variation of 5.51% and 10.63%. Microbial diversity and decay stage directly affected the litter mass-loss rate, with meteorological factors (precipitation, relative humidity, air temperature, and sunlight intensity) being indirect. Our findings highlight the importance of microbial diversity for leaf litter decomposition and the influence of meteorological factors.