Pod and seed weight per plant (PSW) is one of the most important components of soybean yield. We analysed 147 recombinant inbred lines (RILs) of soybean. Using a combination of simple sequence repeat (SSR) and specific-length amplified fragment (SLAF) high-density maps, we applied composite interval mapping (CIM) and multiple interval mapping (MIM) to map quantitative trait loci (QTLs) for PSW across multiple years (2006–10 and 2013). We mapped 24 QTLs for PSW, with 10 QTLs identified by SSR genetic map and 14 by SLAF genetic map. Five consensus QTLs were integrated, and they were validated by a chromosome segment substitution line (CSSL) population. Furthermore, the functions of all genes located in consensus QTL intervals were predicted; nine candidate genes function directly or indirectly in regulating seed development as well as seed size and weight. Our results lay a foundation for the cloning of candidate genes related to PSW and marker-assisted breeding in soybean.