Abstract: The symbiotic model established between rhizobia and soybeans provides the necessary nitrogen for soybean growth and development. In the establishment of symbiosis, type Ⅲ effector factors of rhizobia is one of the important signaling molecules that affect nodulation. In order to elucidate the role of type Ⅲ effector factors of rhizobia in nodulation, this study identified TtsI mutants for nodulation and conducted transcriptome analysis of nodules, as well as enrichment analysis of differentially expressed genes. The results showed that the TtsI mutation（HH103ΩTtsI） could reduce the nitrogenase activity of Suinong 14 nodules, but did not affect the nitrogenase activity of wild soybean ZYD00006 nodules. And after the HH103ΩTtsI, some of the Suinong 14 nodules encoded nitrogen transport related genes and NLP7 were down regulated. Moreover, compared with the inoculation of HH103, there was no significant difference in the relative expression of Glyma.11G235200 and NLP7 in the ZYD00006 nodules. Finally, GO enrichment, KEGG enrichment, and GSEA enrichment analysis showed that differential genes mainly involve signal transduction and metabolic processes. The differential genes were mainly enriched in plant hormone signaling and MAPK signaling pathway. This study provides new ideas for the analysis of the functions and mechanisms of subsequent Type Ⅲ effector factors, as well as the design of efficient nitrogen fixation in soybeans. At the same time, based on the expression differences of nitrogen transport related genes, theoretical support can be provided for further breeding of soybean varieties with high nodulation, high nitrogen fixation efficiency, and high nitrogen utilization efficiency.