Leaf morphology, as a critical measure of plant architecture, has been associated with soybean yield and quality. As yet, conclusive investigations into the genetic basis and biological significance of heteroblasty in soybean remain sparse. To identify and biologically characterize the quantitative trait loci (QTLs) influencing heteroblasty in soybean, 11 traits associated with leaf morphology, seed quality, and grain yield were observed for two recombinant inbred line (RIL) populations grown in two environments. Values of broad-sense heritability (H2) for leaf traits in two RIL populations varied from 0.62 to 0.99. These high heritabilities, taken together with the Kurtosis and Skewness values indicate that the phenotypic variation in leaf morphology observed for both RIL populations are mainly controlled by quantitative traits. The three observed leaf morphology traits exhibited significant correlations (P < 0.05) with more than half of the grain yield and seed quality traits, with correlation coefficients varying from − 0.40 to 0.43, which suggests that leaf morphology can significantly influence soybean yield and quality. A total of 11 QTLs were detected for leaf morphology, with logarithm of odds (LOD) values ranging from 3.40 to 89.6, which accounted for 1.38 ~ 74.53% of genetic variation. Eight of these loci for leaf morphology co-located with those for seed quality and grain yield, which coincided large and extensive leaf morphologies that contributed to seed quality and grain yield formation. Overall, these results provide important information for breeding high yielding crop varieties with improved quality traits produced through optimization of leaf morphology.