Sweetpotato breeding is challenging due to its genetic complexity, and marker-assisted breeding tools are needed to facilitate the improvement of this crop. In the present study, we identified quantitative trait loci (QTL) for storage root yield of sweetpotato using a mapping population consisting of 202 individuals derived from a cross between Xushu18 (a high yield cultivar) and Xu781 (a low yield line). Two parental linkage maps based on AFLP and SSR markers were constructed using this mapping population. Interval mapping (IM) was performed first and, subsequently, a multiple QTL model (MQM) was used to refine the position and magnitude of the QTL. A total of nine major QTLs for storage root yield were mapped, explaining 17.7–59.3% of the variation. These 9 QTLs, YIEF_1, YIEF_2, YIEF_3, YIEF_4, YIEM_1, YIEM_2, YIEM_3, YIEM_4 and YIEM_5, were co-localized to markers E24M1-17d, E53M30-12d, C27_8s**, E63M3-10d, E50M49-4d, IB_S10_9d, E54M5-4d, E21M8-23d and IB_S10_4d, respectively.