To reveal the seasonal effects of different fertilization methods on soil microbial community，the soil microbial community structure and composition in a tea garden under conventional fertilization(CF)and bio-organic fertilizer combined with controlled-release compound fertilizer(MC)were analyzed by metagenomic sequencing at three dates from winter to summer[Nov 14(CF1，MC1)，Mar 1(CF2，MC2)，and May 15(CF3，MC3)]. The results showed that 311211956 high-quality reads and 1763759 Unigenes were obtained. The principal component and correlation analysis showed that the soil microbial gene abundances of MC1 and CF1 treatments were clustered into one category，while the other treatments were clustered into one category，respectively. In different seasons，bacteria，archaea and fungi of CF and MC accounted for 88%-89%，0.8%-2.0% and 0.02%-0.10% of total microorganisms，respectively. The number of archaea gradually was increased，while fungal number was first increased and then decreased. The bacterial and fungal abundances of CF2 and CF3 treatments were significantly lower than that of MC2 and MC3 treatments，respectively，with the opposite abundance of archaea. The number of archaea was higher in CF2 and CF3 treatments than in MC2 and MC3 treatments，respectively，while fungal number was reversed. Significant differences in the abundances of bacteria，archaea and fungi were observed among MC1，MC2 and MC3 treatments，but not between CF1 and CF3 treatments. At the phylum level of bacteria，compared with CF treatment，MC treatment had higher relative abundance of Proteobacteria，Actinobacteria，Gemmatimonadetes，Chloroflexi，Bacteroidetes，Nitrospirae and Armatimonadetes，as well as lower relative abundance of Acidobacteria，Verrucomicrobia and Planctomycetes. Among the archaea taxa，MC resulted in higher relative abundance of Thaumarchaeota，as well as lower relative abundance of Euryarchaeota，Crenarchaeota and Candidatus Bathyarchaeota. Among the fungal taxa，MC treatment induced higher relative abundance of Trichoderma，Tracheomycetes and Cryptomycetes，as well as lower relative abundance of Staphylinidae. Generally，the seasonal change trend of the relative abundance of the dominant bacterial phylum，archaebacterial phylum and fungal phylum showed acertain degree of differences in CF and MC treatments. These results indicated that changes in soil microbial community structure and composition in tea garden were probably both season- and fertilization method-dependent. Bio-organic fertilizer combined with controlled-release compound fertilizer increased bacterial abundance and fungal number and abundance，decreased archaea number and abundance，and influenced soil dominant flora composition. These findings provided an important resource for making full use of microbial resources and improving nutrient utilization of tea plants.