Cultivated soybean (Glycine max), a significant oil and protein source, was domesticated from wild soybean (G. soja). Key traits of domestication syndrome underlying developmental evolution mechanisms remain poorly understood. In this study, cultivated soybean statistically flowered earlier than wild soybean, which correlated with 100-seed weight, implying that developmental heterochrony may be related to fruit/seed size variation during domestication. We compared fruit morphology and development and transcriptomic profiles in developing seeds between cultivar ‘Suinong 14’ (SN14) and wild soybean ‘ZYD00006’ (ZYD06), which exhibited similar flowering times. ZYD06 pods reached their ultimate size earlier than SN14, and the time to maximum fresh weight and seed maturation was longer in SN14 than in ZYD06. Cell division/expansion activities and the expression of related genes in developing pods/seeds were extended in SN14 relative to ZYD06. Differentially expressed genes (DEGs) related to cell division/expansion activities and oil/protein synthesis were enriched in developing seeds between SN14 and ZYD06. Integrated analyses of DEGs, gene co-expression networks, and quantitative trait loci revealed new candidate genes for soybean seed size variation. Transgenic Arabidopsis lines overexpressing Glyma.17G090200, which encoded a RING-finger E3 ubiquitin-protein ligase, showed an increased seed weight. Our findings suggest that heterochrony is a principal evolutionary developmental mechanism underlying soybean domestication, providing new insights and resources for soybean breeding and genetic improvement.