High temperature severely constrains soybean growth and development, leading to significant yield losses. The development of high-temperature tolerant cultivars necessitates the identification of elite germplasm with such tolerance. Here, we evaluated the phenotypic variation among 608 soybean accessions grown under natural high-temperature conditions by measuring key traits over three years, from 2018 to 2020. These traits included plant height, first pod height, number of main stem nodes, number of branches, number of pods per plant, seed weight per plant, and 100-seed weight. Analysis of variance indicated that temperature was a major factor driving variation, particularly affecting the number of branches, seed weight per plant, and 100-seed weight. High temperature sensitivity among accessions was assessed by calculating high-temperature response correlation coefficients and integrating principal component analysis, fuzzy membership function analysis, and cluster analysis. Compared with the control group, the high temperature group exhibited a significant increase the number of main stem nodes. However, first pod height, number of branches, number of pods per plant, seed weight per plant, and 100-seed weight decreased significantly. Principal component analysis transformed the high temperature response correlation coefficients of six traits into three principal components, which accounted for a cumulative contribution rate of 74.23%. Using the weights of each principal component, we calculated a composite high-temperature sensitivity index (T-value). Cluster analysis classified the 608 accessions into five sensitivity classes: extremely sensitive (8 accessions), slightly sensitive (123 accessions), moderately sensitive (309 accessions), mildly sensitive (158 accessions), and non-sensitive (9 accessions). Notably, foreign high temperature tolerance germplasms, including Kanto 102, Suzumaru, Bedford, and PI80828-1 were identified as promising candidates. This study providing germplasm resources and theoretical support for breeding new high temperature tolerant soybean varieties.