Lower temperature tolerance (LTT) and growth traits are vital to the success of overwintering scallop farming in the North China Sea. Bohai Red, a novel selected scallop strain and the main aquaculture species in this region. However, its poor LTT hinders its growth. To improve these characteristics, the larger Bohai Red scallop was crossed with the smaller bay scallop which tolerates low temperatures. The full-sib F1 hybrids and the whole-genome resequencing (WGR) method were used to construct a high-density genetic linkage map comprising 5,925 single nucleotide polymorphisms. To the best of our knowledge, the present work is one of the first to fine map the LTT and growth-related QTLs in a genetic linkage map for hybrid spp. scallops.