The Cd-tolerant endophytic bacteria R3(Pantoea sp.) and R5(Stentrophomonas sp.) suspensions were applied to Huanghuazhan rice(CK was not added to endophytic bacteria suspension) grown in greenhouse. The absorption of cadmium by endophytic bacteria in the aboveground and underground parts of rice plants was studied. The amount of accumulation and 16S rDNA sequencing were used to study the changes of endophytic bacterial community structure in the aboveground and underground parts of rice plants. The results showed that R5 and R3 strains could significantly reduce the contents of cadmium in different parts of rice plants at the peak tillering stage. After treatment in R5 and R3, the endophytic bacterial community structure of rice plants changed significantly. The diversity of endophytic bacterial community increased in the aboveground part of rice, but decreased in the root part of rice. The relative abundance of Escherichia/Shigella and Acetobacter in rice plants increased significantly, and the R5 strain could colonize successfully into the stems and sheaths of the rice.