Peanut is one of the important oilseed crops in China. Breeding for high yield is an important target. Seed size and shelling percentage are the factors effecting of peanut yield. QTL mapping for seed size and analyzing its relationship with shelling percentage will lay a foundation for high yield molecular breeding. In this study, the seed size of a recombinant inbred line (RIL) population (Xuhua 13 × Zhonghua 6) were investigated at three consecutive years. The seed length (SL), seed width (SW), and hundred seed weight (HSW) were variable in RIL population, and a significant positive correlation was detected among them. 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-localized and they 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. In conjugation with the QTL mapping result of shelling percentage, co-localized QTL and specific QTL for either trait were found. Collectively, this study laid a foundation for future fine mapping, molecular marker-assisted breeding and synergistic improvement of high yield in peanut.