Irrational Eucalyptus plantation could induce the degradation of soil quality. A field experiment was conducted to investigate the effects of green manure intercropping on soil nutrient, enzyme activity and bacterial community in Eucalyptus urophylla × Eucalyptus grandis plantation in order to guide Eucalyptus sustainable production, in which three treatments of Tephrosia candida (TC), Sesbania cannabina (SC) and control without green manure (CK) were setup. The results show that both TC and SC increase soil available nutrients, enzyme activity and microbial biomass. The relative abundances of Firmicutes, Chloroflexi,Oxobacter, Ruminiclostridium and Candidatus Solibacter are higher under SC, while those of Proteobacteria and Thermincola are higher under TC. TC greatly influences nitrogen fixation and nitrate reduction related bacteria, while SC significantly affects aromatic compound degradation related bacteria. Soil available boron is the main factor influencing soil microbial mass and enzyme activity, while soil alkaline hydrolysis nitrogen is the main factor affecting the abundances of bacteria in phylum and family levels. In conclusion, green manure intercropping can improve soil nutrient, increase soil enzyme activity and regulate soil microbial structure, thus it is an effective measure for Eucalyptus sustainable production.