The yield reduction caused by soil salinity is an increasing problem for agriculture worldwide. Salt stress hampers plant growth, and affects plant reproduction and survival. In addition to the salt response signaling pathways in plant cells, diverse rhizosphere microbes have been reported to enhance plant salt tolerance. However, our knowledge of halotolerant microbial species and the salinity mitigation mechanisms remains limited. Here we analyzed the survival rates and growth phenotypes of 120 wild and cultivated soybean germplasms at the saline land in Dongying, China, and isolated the rhizosphere microbiota from five salinity-tolerant and five salinity-resistant soybean germplasms. We then characterized the taxa profiles and the enriched functional pathways of the rhizosphere microbiota by metagenomics. Results showed that salinity-tolerant soybean plants had more diverse and intricate rhizosphere microbial communities than salinity-sensitive soybeans. Intriguing, besides rhizobia, the most enriched rhizosphere microbial genus for all five salinity-tolerant soybeans was Pseudomonas, while for four out of five salinity-susceptible soybeans was Hydrogenophaga. Pathways such as the citrate cycle, oxidative phosphorylation, and carbon fixation were enriched in salinity-tolerant soybeans, suggesting enhanced energy dynamics. Further analysis showed that a bacterium strain Iso1.8 which was enriched in the rhizosphere of salinity-tolerant soybeans could significantly enhance the nitrogen fixation rate of soybean compared to the control after salt treatment, and promote soybean growth by increasing seedling height and chlorophyll content. In summary, we revealed the rhizosphere microbial taxa and functional profiles of either salt-tolerant or salt-susceptible soybeans, and identified a bacterium strain with plant growth and fitness promoting ability.