Increasing planting density is among the most effective ways to increase soybean yield, but high planting density increases lodging risks in soybean plants. To examine the effects of shading on soybean plant lodging, the tall cultivar Heinong 48 (HN48) and dwarf cultivar Henong 60 (HN60), two soybean cultivars with large plant height differences (approximately 40 cm), were selected, and their internode lengths were measured under different planting densities in 2019 to determine the key internode influencing lodging. In 2020, we treated soybean plants with different shading treatments to examine the morphology, anatomical structure and stem fiber composition of the fifth internode, changes in the GA3 (gibberellic acid) content, and relative expression of GA3-related enzyme genes in the stem under different shading conditions. The results showed that as the planting density increased, the lengths of the internodes changed significantly, starting from the fifth internode. Under different shading conditions, the length of the fifth internode increased for both cultivars, but the diameter and the diameter-to-length ratio decreased; the area of the xylem decreased, and the pith cells stretched more longitudinally and were more orderly; the lignin, cellulose, and hemicellulose contents decreased; the GA3 content in the stem increased, and the expression levels of GmGA3ox6, GmGA20ox1-D, and GmGA2ox4 enzyme genes were all upregulated; and the change in PSN treatment was more significant than other treatments. Therefore, the fifth internode was the key internode that affected lodging in soybean plants, shading could increase the GA3 content significantly in soybean stems, and the increase in GA3 content was positively correlated with the shaded area. This study provides a new direction for future research on lodging resistance in densely planted or intercropped soybean plants.