Red soil and cinnamon soil were collected from Chenzhou of Hunan and Gongyi of Henan, respectively. Soils were treated with Cu(NO3)2, Zn(NO3)2 or Cd(NO3)2, respectively, for two weeks. Rhizobium fredii strain HN01 was inoculated into the two soils polluted with three heavy metals. Sequential extraction method was employed to investigate the forms of copper (Cu), zinc (Zn), and cadmium (Ca) in the examined soils with the absence and presence of rhizobia. Results showed that the total amount of solid-bound Zn decreased 10% after the inoculation. The decrease for the amount of Zn associated with carbonate, manganese (Mn) oxides, and organic matter fraction was from 9 to 26%. No significant change was observed for the total amount of Zn combined with solid phase of red soil in the presence of rhizobia. However, the amount of specifically adsorbed and Mn oxides bound Zn decreased, while the amount of exchangeable Zn increased. Inoculation of rhizobia depressed the release of Cu to the soil solution and increased the total amount of Cu associated with solid phase in cinnamon soil. The increase for the amount of exchangeable Cu and the Cu in fractions of carbonate, Mn oxides, and organic matter ranged from 20 to 54%. There was no significant change for the level of Cd in the solution in both soils after rhizobia inoculation. The amount of Cd in the fractions of exchangeable and organic increased 22 and 11%, while that in the fractions of specific and Mn oxides decreased 14 and 29%, respectively. The different influence of rhizobia on the distribution of three heavy metals in two soils was mainly ascribed to the growth status and pH changes exerted by the metabolites of rhizobia. These data are helpful for the understanding of the chemical behavior and biogeochemical cycle of heavy metals affected by microorganisms in soil environment, which is fundamental for heavy metal bioremediation.