The lack of available phosphorus in soil has become the major restricted factor for yield and quality of soybean (Glycine max). Therefore, the mining of genetic loci at crucial phosphorus requirement stages becomes very important for genetic improvements of phosphorus efficiency in soybean. In view of this, the association analysis based on the SoySNP6K (5403 SNP markers) was used in this study to find 10 genetic loci controlling phosphorus related traits of soybean at the crucial stages, with the result that 78 SNPs were detected under normal phosphorus condition at T1 stage (four-leaf stage), of which relatively more were associated with root and total dry weights, and 134 SNPs were detected under low phosphorus condition at T1 stage, of which relatively more were associated with total dry weight, with SNP clusters on chromosomes 8, 13 and 20 detected controlling shoot and total dry weights, shoot fresh and dry weights, and total dry weight. At T2 stage (six-leaf stage), 83 SNPs were detected under normal phosphorus condition, of which relatively more were associated with plant height and shoot dry weight, and 53 SNPs were detected under low phosphorus condition, of which relatively more were associated with plant height and root/shoot ratio, with an SNP cluster on chromomsome 18 detected controlling root and total dry weights, and 3 SNPs on chromomsomes 11, 16 and 18 detected associated with pleiotropism. More importantly, 9 SNPs were detected controlling shoot fresh and dry weights, root/shoot ratio, and plant height at T1 and T2 stages simultaneously, which provided some selected molecular markers for soybean phosphorus efficiency genetic improvements in future.