Soil microbial biomass is the active part of soil organic matter and an important indicator of soil quality and carbon and nitrogen cycling mechanism. The different season (spring, summer, autumn and winter) and soil layer (0-10, 10-20, 20-30, 30-40 and 40-50 cm) variations of soil microbial biomass carbon (SMBC, mg/kg) and microbial biomass nitrogen (SMBN, mg/kg) and their influencing factors were studied in alpine meadow of the Shule River headwater region in the northeast margin of Qinghai-Tibet Plateau. The results showed that (1) the SMBC of different soil layers increased gradually in spring, peaked in summer, decreased in autumn, and reached the minimum value in winter. While the SMBN decreased gradually in spring, reached the minimum value in summer, increased in autumn, and peaked in winter. (2) Both SMBC and SMBN decreased with the increase of soil depth. The 0-10 cm layer of SMBC and SMBN was significantly higher than the 40-50 cm layer. The season variations of SMBC and SMBN in the 0-10 cm layer was also higher than those in the 40-50 cm layer. (3) The SMBC/SMBN in the 0-50 cm layers increased gradually in spring, peaked in summer, decreased in autumn, and reached the minimum value in winter. Its season variation range was 8.77-23.59, which was at a relatively high level. (4) The season and layer variations of SMBC, SMBN and SMBC/SMBN were mainly influenced by belowground biomass of vegetation and soil temperature. (5) The SMBC/SOC in different soil layers increased gradually in spring, peaked in summer, decreased in autumn, and reached the minimum value in winter. While the SMBN/TN decreased gradually in spring, reached the minimum value in summer, increased in autumn, and peaked in winter. Except that there was no significant difference in soil layer variation in summer, SMBC/SOC and SMBN/TN showed that the 0-10 cm layer was significantly higher than the 40-50 cm layer. (6) In the 0-50 cm layers, SMBC/SOC was significantly higher in summer and autumn than that in winter and spring. Its season variation range was 0.58%-1.18%. while SMBN/TN was significantly higher in autumn and winter than in summer and its season variation range was 0.39%-0.72%. In conclusion, the variations of season and profile depth could affect SMBC and SMBN contents significantly. The 0-10 cm soil layer has the strongest accumulation ability on SMBC and SMBN.