Soybean (Glycine max) is one of the most important economic legume crops with largest planting area, and is also an important oil crop, as well as food and feed material. Soybean-rhizobia symbiosis plays important roles in plant cultivation and fertilizer application. However, there are many problems in agricultural application of soybean symbiotic nitrogen fixation. In this review, we summarized three restriction factors (host specificity, low nitrogen fixation efficiency and abiotic stress) and discussed research progresses of these factors. Clarification of host specific mechanism will help to select and apply rhizobia inoculants. Both maintaining high nitrogenase activity and delaying nodule senescence can improve the efficiency of symbiotic nitrogen fixation. Abiotic stress-tolerant rhizobia can improve the abiotic stress tolerance of soybean. Breeding stress tolerant genotypes of soybean and rhizobia, obtaining correlated genes are the common strategies to improve soybean symbiotic nitrogen fixation under extreme conditions. Regulatory mechanisms of these restriction factors are still poorly understood and needs further clarification.