This study firstly examined the quality and safety profiles of scallop Chlamys farreri cultured, a major bivalve species cultured along the coast of the Shandong province. Samples were collected from 10 different regions in the Shandong peninsula, and then, the nutrient components, including proximate, amino acids, fatty acids, mineral elements, and vitamins, as well as primary biological and chemical hazards, such as banned antibiotics, organic pollutants, heavy metal, shellfish toxins, and pathogenic bacteria in Chlamys farreri were analyzed. The comprehensive indexes contain almost 70 chemical and microbial hazards and 90 kinds of nutritional and flavor substance. A comprehensive evaluation method was established to ascertain major nutrient quality characteristics, including amino acid score, fatty acid score, taste activity value, equivalent umami concentration and nutrient index. Feature indicators were comprehensively evaluated using correlation analysis, system cluster analysis, orthogonal partial least squares discriminant analysis, and factor analysis. On the basis of 17 characteristic component filtered from 33 significant differential indexes, the quality of Chlamys farreri from different regions was ranked by factor analysis. The factor analysis score shows that Xunshan > Laoshan > Changdao > Kongtongdao > Yangmadao > Yuanyao > Rushan > Shidao > Shuangdao > RenJiatai.