Plant height (PH) is an important agronomic trait affecting crop yield and quality. In this study, a soybean collection of 192 natural accessions and 1536 single nucleotide polymorphism (SNP) makers were used to identify genomic regions associated with PH. There is a large genetic variation in PH with a diverse panel. Three phenotypic indexes (PH measured at six stages, the conditional PH, and the relative growth rates of PH) were used to identify developmental behavior for PH in soybean. Six methods were used to minimize false-positive associations in association mapping, and finally the generalized linear model for principal component analysis had been used in this study. Three SNPs, BARC-040651-07807, BARC-030433-06867, and BARC-042475-08274, were highly significantly associated with PH in the final growing period, and two SNPs, BARC-038795-07333 and BARC-013749-01246, were connected with PH in the early growing period.