[Objective] To investigate the role of ABC transporter permease gene atpA in the symbiotic nitrogen fixation between Rhizobium and legumes in Mesorhizobium huakuii 7653R. [Methods] An atpA gene mutant was obtained through single exchange insertion mutation, and studied its functions on the growth and symbiosis of Astragalus sinicus L. [Results] Deletion of the atpA gene caused the Rhizobia to enter the stationary phase earlier and weakened their biofilm formation ability. Plants inoculated with the mutant strain exhibited yellowing leaves and pronounced nitrogen deficiency symptoms. These plants showed a decrease in plant height, fresh weight of above-ground parts, number of nodules, and nitrogen-fixing enzyme activity by 14.3%, 33.3%, 31.5%, and 18.8%, respectively. Proteomic analysis identified 78 differentially expressed proteins. Compared with wild-type bacteroids, 23 proteins were up-regulated and 55 proteins were down-regulated in the atpA gene mutant bacteroids. Among these differentially expressed proteins, 10 were related to amino acid transport and 12 were associated with the formation of the nitrogen-fixing complex in nodules. [Conclusion] The ABC transporter permease gene atpA in Mesorhizobium huakuii plays a crucial role in its growth and symbiotic relationship with the host plant Astragalus sinicus L.