Soybean (Glycine max (L.) Merrill) is one of the most important crop plants in the world as an important source of protein for both human consumption and livestock fodder. As flowering time contributes to yield, finding new QTLs and further identifying candidate genes associated with various flowering time are fundamental to enhancing soybean yield. In this study, a set of 120 recombinant inbred lines (RILs) which was developed from a cross of two soybean cultivars, Suinong4 (SN4) and ZK168, were genotyped by genotyping-by-sequencing (GBS) approach and phenotyped to expand the cognitive of flowering time by quantitative trait loci (QTL) analysis. Eventually, three stable QTLs related to flowering time which were detected separately located on chromosome 14, 18, and 19 under long-day (LD) conditions. We predicted candidate genes for each QTL and carried out association analyses between the putative causal alleles and flowering time. Moreover, a transient transfection assay was performed and showed that NUCLEAR FACTOR YA 1b (GmNF-YA1b) as a strong candidate for the QTL on chromosome 19 might affect flowering time by suppressing the expression of FLOWERING LOCUS T (GmFT) genes in soybean. QTLs detected in this study would provide fundamental resources for finding candidate genes and clarify the mechanisms of flowering which would be helpful for breeding novel high-yielding soybean cultivars.