Increasing planting density has become an effective way to improve soybean yield. However, the comprehensive evaluation system to identify density-tolerant soybean germplasm resources has not been systematized. This study attempts to construct an evaluation method based on multi-year data, followed by evaluating the density-tolerant characteristics to identify the elite soybean germplasm. Seventy-seven soybean germplasm resources suitable for Huang-Huai-Hai ecological area were sown with two densities including high-density sowing (plant spacing 8.0 cm, about 315,000 plants/ha) and conventional density sowing (plant spacing 13.0 cm, about 195,000 plants/ha). The evaluation of dense planting tolerance was conducted by obtaining nine relevant character indexes in two calendar years (2019 and 2020). Compared with the conventional planting density, the height of gravity center and bottom pod of the plant were significantly increased (P < 0.01) and (P < 0.05), respectively, and the number of effective branches and seed weight per plant decreased significantly (P < 0.01) under high planting density. According to the significant correlation coefficient, the principal component and membership function standardization analysis were carried out to estimate the comprehensive evaluation value (M) which was deployed for the clustering analysis. The dense planting tolerance characteristics were divided into five types (I, less dense type; II, strong less dense type; III, intermediate type; IV, strong dense type; V, dense type). Three soybean varieties (Wuxing 1, Motte*, and Gaozuoxuan 1) qualified for condensed planting were preliminarily identified. Collectively, this study established a density-tolerant evaluation method useful for developing new dense-planting varieties and studying their physiological mechanism in soybean.