design: Soybeans come from the southwestern of China, namely Yunnan Province, Guizhou Province, Sichuan Province and Chongqing. This project conducted whole-genome resequencing on 202 soybeans with an average sequencing depth of 4X. Simultaneously, in the soybean monoculture and maize/soybean relay intercropping systems, phenotypic traits including plant height, number of main stem nodes, number of branches, branch length, internode diameter, breaking strength, seed oil content and so on of soybeans were measured before the harvest of maize and at maturity, providing fundamental data for comprehensively elucidating the molecular mechanisms underlying these traits in soybeans.