<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>In this study, 308 representative soybean lines from a core collection and 168 F<jats:sub>9</jats:sub> soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80–26.10% of phenotypic variation. Intriguingly, only two loci, <jats:bold><jats:italic><jats:underline>Loc11</jats:underline></jats:italic></jats:bold> and <jats:bold><jats:italic><jats:underline>Loc19–1</jats:underline></jats:italic></jats:bold>, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.</jats:p> </jats:sec>