Abstract: Endophytic bacteria have become an important part of microecosystem, endophytic bacteria and Rhizobia commonly coexist in the special nodule habitat. The relationship differences of endophytic bacteria and Rhizobia in root nodule and host was compared. Combined with group research, the types, the host and the adaptability of soybean nodule endophytes, functional diversity of soybean root nodule endophytes including biological nitrogen fixation, promoting plant growth, enhancing host stress resistance, disease resistance and ability of combined remediation to environmental pollution were summarized. Based on analysis above, author pointed out the research direction of soybean nodule endophytes, to further promote plant growth and develope sustainable agriculture.