As soybean is highly sensitive to photoperiod, and the cultivation area of soybean is restricted to a narrow latitude region. The adaptability of soybean growth across wide latitude areas is owing to the rich variations of genes conditioning the flowering time and maturity. Identification of new quantitative trait loci (QTLs) and validation of the potential genes are beneficial to clarify the complex regulatory network in the photoperiod pathway. In the present study, high-density genetic maps were performed using genotyping-by-sequencing (GBS) with two recombinant inbred line (RIL) populations developed from the crosses between cultivated soybean varieties, Noir × Archer (NA) and Noir × M336-1 (NM) for evaluating the traits of flowering time (R1), maturity (R8), and reproductive period (RP) under long-day (LD) conditions. In total, we identified four stable QTLs on chromosomes 4, 6, 18, and 19 in NA and NM RILs. The QTLs on chromosomes 6 and 19 corresponded to the maturity genes E1 and E3, respectively. Another major QTL on chromosome 18 was detected in both NA and NM populations and played pivotal roles in the regulation of flowering time, maturity, and reproductive period. The QTL mapped to chromosome 4 was shown to mainly regulate the maturity time by affecting the post-flowering stage in NA population. The results in this study will provide new loci and fundamental resources to elucidate the genetic basis related to flowering, maturity, and reproductive period and will be helpful for further research on soybean flowering and molecular breeding under LD conditions.