Scallop is a popular sea food and an important aquaculture shellfish. Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding. Myostatin (MSTN) is a conservative regulator of muscle growth, and has become one of the most important target genes for genetic improvement of the production of farmed animals. In this study, four single nucleotide polymorphisms (SNPs) were identified in the 5’ flanking region of MSTN gene (CfMSTN) in Zhikong scallop (Chlamys farreri). The association of these SNPs with scallop growth traits, including shell length, shell height, body weight and striated muscle weight was analyzed. The SNP g-1162G<T was found to associate with shell length, shell height, and striated muscle weight. The TT type scallops showed significantly higher trait values than those of GT type, and the GG type individuals exhibited median values. On the contrary, significantly more CfMSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones. Our results suggested that CfMSTN might regulate the scallop muscle growth negatively, and SNP g-1162G<T can be used as a candidate marker for the selective breeding of high-yielding scallop.