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Yesso scallop (Patinopecten yessoensis) is one of the most economically important shellfish in aquaculture industry of China, and improving growth rate has become a central task of the Yesso scallop farming industry. By far, genetic studies on Yesso scallop growth are very limited and there is no systematic screening of the growth-related genes or loci for this species. In the present study, we conducted a genome-wide association study (GWAS) for six growth traits of Yesso scallop utilizing over nine thousand single nucleotide polymorphism (SNP) markers. Two significantly growth-associated SNPs were identified and the SNP showed the lowest P value was located in E2F transcription factor 3 (E2F3), the gene being reported as important regulator of cell proliferation and cell cycle. Further analysis in another population identified a new growth-associated SNP in this gene. Moreover, two tandemly repeated E2F3s (PyE2F3-1 and PyE2F3-2) were found at this locus, and PyE2F3-1 expression was significantly correlated with the values of shell length, shell height, body weight, and adductor muscle weight in Yesso scallop. Our data suggest that PyE2F3-1 might be a positive regulator of shell and soft tissues growth, and it could be a candidate gene for Yesso scallop breeding aiming at growth improvement.