The Pacific oyster(Crassostrea gigas) is cultured worldwide, and the meat yield and shell shape (shell width and shell depth) are two of the most important economic traits of this species. The mapping population used in this study was an F1 full-sib family produced by mating a female parent from a second-generation strain selected for rapid growth in Japan with a male parent from a wild Chinese population. Eighty-three progeny were selected for linkage analysis in July 2009, and the meat yield, shell width, and shell depth traits were determined. The values for the shell width and shell depth traits were normally distributed, except meat yield, and these three traits were positively correlated. A genetic linkage map was constructed with 120 microsatellite and 66 single nucleotide polymorphisms (SNPs) from the F1 full-sib family. Based on the linkage map, PROC QTL 2.0 software was selected to perform a quantitative trait locus (QTL) analysis for the meat yield and shell shape (shell width and shell depth) traits under a four-way model using the maximum-likelihood method. The results show 13 related QTLs distributed on three linkage groups (LGs). Four QTLs were associated with meat yield on LG 1 and 3 and explained 0.25%–47.53% of the phenotypic variance. Three QTLs on LG10 were related to shell width and explained 0.71%–45.39% of the phenotypic variance. Six QTLs were identified for shell depth on LG10 and explained 3.37%–24.78% of the phenotypic variance. The results of the QTL linkage group and correlation analyses suggest that meat yield and glycogen content, and shell depth and shell width may have closely related genetic characteristics, and that the traits (meat yield and glycogen content, and shell depth and shell width) could be improved simultaneously when closely linked markers are used during breeding. These results provide a useful reference for further candidate gene research and molecular marker-assisted selection in the Pacific oyster.