In the present study, we constructed an "applied core collection" for phosphorus (P) efficiency of soybean germplasm using a GIS-assisted approach. Systematic characterization and comparative analysis of root architecture were conducted to evaluate the relationship between mot architecture and P efficiency and its possible evolutionary pattern. Our results found that: I) root architecture was closely related to P efficiency in soybean. Shallow root architecture had better spatial configuration in the P-rich cultivated soil layer hence higher P efficiency and soybean yield;ii) there was a possible co-evolutionary pattern among shoot type, root architecture and P efficiency. The bush cultivated soybean had a shallow root architecture and high P efficiency,the climbing wild soybean had a deep root architecture and low P efficiency, while the root architecture and P efficiency of semi-wild soybean were intermediate between cultivated and wild soybean; iii) P availability regulated root architecture. Soybean roots became shallower with P addition to the topsoil, indicating that the co-evolutionary relationship between root architecture and P efficiency might be attributed to the long-term effects of topsoil fertilization. Our results could provide important theoretical basis for improving soybean root traits and P efficiency.