Soil bacteria and fungi are the ultimate driver of the biogeochemical cycling of carbon (C) and nutrient in soils. We applied a microbial-explicit model – the CLM-Microbe – to investigate the dynamics of fungal (FBC) and bacterial (BBC) biomass C at the global scale during 1901-2016. We first evaluated the performance of the CLM-Microbe model in reproducing the spatial patterns of FBC and BBC in the top 30 cm and microbial biomass C (MBC) in 0-1 m, vegetation variables including gross (GPP) and net (NPP) primary productivity, and soil variables comprising heterotrophic (HR) and soil (SR) respiration and dissolved (DOC) and soil organic C (SOC) in the top 30 cm and 1 m. The CLM-Microbe model was able to reproduce global averages and latitudinal trends of those variables. In addition, the CLM-Microbe model captured the grid-level variation in GPP (R2=0.78), NPP (R2=0.63), SR (R2=0.26), HR (R2=0.23), DOC in 0-30 cm (R2=0.2) and 0-1 m (R2=0.22), SOC in 0-30 cm (R2=0.36) and 0-1 m (R2=0.26), FBC (R2=0.22) and BBC (R2=0.32) in 0-30 cm, and MBC in 0-1 m (R2=0.21). From the 1900s to 2007-2016, the global budget of FBC and BBC increased, with FBC and BBC increased by approximately 1.0 PgC and 0.4 PgC in 0-30 cm and 1.5 PgC and 0.8 PgC in 0-1 m, respectively. Increases in FBC and BBC (0-30 cm and 0-1 m) were larger at northern high latitudes and in equatorial regions than at other latitude. By continent, the largest absolute increases of FBC and BBC (0-30 cm and 0-1 m) were in Asia and South America, particularly in eastern Asia and central and northern South America. However, the largest relative increases of FBC and BBC differed, with the largest relative increase of FBC (0-30 cm and 0-1 m) in South America and of BBC (0-30 cm and 0-1 m) in Europe. The historical increase of FBC and BBC was jointly governed by increasing vegetation C input and variations in soil temperature and moisture. This study enhances our understanding of dynamics and controls of fungal and biomass at the global scale over historical period, contributing to the knowledge of variations in soil microbial community under a changing climate.