Little information is available on the seasonal response of soil microbial biomass to climate warming even though it is very sensitive to climate change. A two-year field experiment was conducted in the subalpine and alpine forests of the eastern Tibetan Plateau, China. The intact soil cores from 3,600 m site were incubated in three elevations (3,000 m, 3,300 m and 3,600 m) to simulate climate warming. Soil microbial biomass carbon (MBC) and nitrogen (MBN) were measured at different periods (early growing season [EG], late growing season [LG], onset of soil freezing period [OF], deep soil frozen period [DF] and soil thawing period [ET]) from May 2010 to August 2012. Average air temperature and soil temperature increased with the decrease of elevation during the experimental period. MBC and MBN showed a sharp decrease during the OF and ET in both organic layer and mineral layer at the three sites. Additionally, a relatively high MBC was observed during the DF. MBC and MBN in the soil organic layer decreased with the decrease of elevation but the opposite was true in the mineral soil layer. Warming had stronger effects on soil microbial biomass in the organic layer than in the mineral soil layer. The results indicated that future warming would alter soil microbial biomass and biogeochemical cycling in the forest ecosystems on the eastern Tibetan Plateau.