Soybean is a legume crop rich in protein and oil. Symbiotic nitrogen fixation plays an important role in the growth of soybean. The type-III effectors such as NopT and NopP are the important signaling factors for the establishment of symbiosis in soybean. In this study, the analysis of nodulation in soybean after inoculation with HH103ΩNopT, HH103ΩNopP, and HH103ΩNopT&NopP indicated crosstalking between NopT and NopP. Further, we aimed to identify the genes of soybean involved in the pathway underlying the crosstalk between NopT and NopP using RNA-seq analysis. Five of the identified candidate genes were confirmed to be induced by NopT and NopP. The expression of GmPBS1 significantly increased to a much larger extent than that of the other four genes after soybean was inoculated with HH103ΩNopT, HH103ΩNopP, or HH103ΩNopT&NopP. The interaction between NopT and GmPBS1 was confirmed via bimolecular fluorescence complementation. Finally, nodulation analysis after GmPBS1 overexpression in the hairy roots indicate that GmPBS1 can regulate the negative effect of NopP on the nodulation, and this regulation is related to NopT. Collectively, our results suggested that during the nodulation in soybean, NopT and NopP have a crosstalking network and GmPBS1 is the hub gene.