Soybean (Glycine max L. Merr.) is a globally significant oilseed crop. The number of four-seeded pods in the lower part (FSPL) serves as a critical yield component under high-density planting. To date, numerous crop-specific traits have been investigated in multiple breeding studies of soybean; however, little attention has been paid to studies on FSPL. Hence, in this study, we investigated the genetic basis of FSPL using a recombinant inbred line population (RIL3613) across four environments. The segregated genetic mapping population was cultivated during the field experiments, and the collected phenotypic dataset of FSPL exhibited quantitative genetics and high broad-sense heritability (0.724), indicating stable genetic control. Further, we performed quantitative trait locus (QTL) mapping using raw means in each environment and identified 10 QTL, explaining phenotypic variations (PVE) ranging from 0.10% to 2.94%. Among the identified environmentally stable QTL, qFSPL-15-1 was consistently detected across all environments. Two candidate genes [Glyma.15G034100 (encoding lysophosphatidic acid acyltransferase 2) and Glyma.15G034200 (encoding an RNA-binding protein)] were predicted within the flanking genomic interval. The allele frequencies of haplotype combinations of Hap1: Pro2 + CDS1 for Glyma.15G034100 and Hap3: Pro3 + CDS1 for Glyma.15G034200 in wild soybeans (26.6–30.0%) were larger than improved cultivars (52.6–53.4%). We believe that our current findings elucidate the molecular mechanisms regulating lower-pod formation and provide precise genetic targets for marker-assisted selection in high-yield soybean breeding.