Soil microbes are important components of soil ecosystem, and they are also one important index for soil fertility, and they can play great roles in material circulation and energy flow in ecosystem. Nitrogen deposition can influence the growth and proliferation of microorganisms, which can change the community structure and function, and then affect the material circulation and energy flow of soil ecosystem. Nitrogen deposition was simulated in laboratory, and the effects of nitrogen deposition on the soil microbes were examined with phospholipid fatty acids technique with different tree species, namely Schima superba, Ormosia pinnata, Pinus massoniana and Acacia mangium. The results showed that bacteria, over 40% of soil microbial biomass, was the main component of soil microbial biomass at current nitrogen deposition. Both sampling times (P<0.01) and tree species (P<0.05) had significant effects on the total soil microbial biomass and bacteria biomass. Soil microbial biomass (the total soil microorganisms, bacteria, fungi and actinomycetes) in October were higher than those in April for the same tree species, with the highest for Acacia mangium (total soil microbial biomass was 76.78 nmol·g~(-1), bacteria biomass was 33.94 nmol·g~(-1), fungi biomass was 6.91 nmol·g~(-1), actinomycetes biomass was 8.38 nmol·g~(-1)) and the lowest for Schima superba (total soil microbial biomass was 57.89 nmol·g~(-1), bacteria biomass was 24.79 nmol·g~(-1), fungi biomass was 4.16 nmol·g~(-1), actinomycetes biomass was 5.57 nmol·g~(-1)) in April, and the highest for Ormosia pinnata (total soil microbial biomass was 92.67 nmol·g~(-1), bacteria biomass was 38.85 nmol·g~(-1), fungi biomass was 8.09 nmol·g~(-1), actinomycetes biomass was 9.27 nmol·g~(-1)) and the lowest for Schima superba (total soil microbial biomass was 71.10 nmol·g~(-1), bacteria biomass was 30.79 nmol·g~(-1), fungi biomass was 4.90 nmol·g~(-1), actinomycetes biomass was 7.04 nmol·g~(-1)) in October. Actinomycete was effected significantly by the interaction of tree species and sampling times (P<0.05). The result also indicated that the total microbial biomass had significantly positive correlation with ammonium nitrogen (P<0.05), however, fungi biomass showed significantly positive correlation with soil organic matter (P<0.01). The results have significant roles on management on the health of ecosystem under global change.