Peanut is one of the important oilseed crops in China. High yield is an important breeding objective. Seed size, and shelling percentage are the factors effecting of peanut yield. QTL mapping for seed size and analyzing their relationship with shelling percentage will lay a foundation for high yield molecularbreeding. In this study, the seed size of a recombinant inbred line (RIL) population ( Xuhua 13×Zhonghua 6) were were investigated for three consecutive years. The result showed that seed length (SL), seed width (SW), and hundred seed weight (HSW) varied widely in RIL population, and there were significant positive correlation among the three traits. Based on the genetic map, 52 QTL were detected with 3.09%-17.34% phenotypic variations explained (PVE), of which qSLA05.2 and qHSWA05.2, qSWA07.1 and qHSWA07 are co-localization major QTLs and can be repeatedly detected in multiple environments. Favorable alleles of qHSWA05.2 and qHSWA07 were derived from the female and male parents, respectively. A combination of the two favorable alleles using the linked markers was verified to increase hundred seed weight by 33.80±1.19g in the RIL population. Combined with the QTL mapping results of shelling percentage, it was found that there were co-localization and specific QTL among the traits. These results lay a foundation for fine mapping, molecular marker-assisted breeding and synergistic improvement of peanut yield.