Family selection has emerged as the essential manner of selective breeding in aquaculture. The current artificial selection for Japanese scallop (Patinopecten yessoensis) is primarily focused on the apparent characters, e.g. growth, shell color and survival rate. However, the selective breeding in terms of nutritional value of adductor muscle has been rarely reported. Based on the adductor muscle dry weight and fatty acid profile of P. yessoensis, the families harboring higher growth rates were screened out initially and the vital nutritional indicators, i.e. the relative abundances of EPA as well as DHA of total fatty acids, and the ratio of ω-3/ω-6 fatty acids, were further assessed. Among a total of 12 selected families, the growth rates and adductor muscle ratio of B04, B05 and B10 were prominently higher than other families. The relative abundances of EPA and DHA of total fatty acids were all above 45% and the ratio of ω-3/ω-6 fatty acids varied between 10.94 and 12.69 in any individual family. The families, B03, B05, B06, B07, B10, B11 and B12, exhibited superior nutritional performance involving fatty acids of adductor muscle. The highest-quality families of P. yessoensis, i.e. B05 and B10, were successfully selected on a basis of the comprehensive comparative analyses. These results revealed that it was feasible to perform artificial selection in terms of the growth performance and the equally critical fatty acid composition of P. yessoensis. This study provides valuable insights into selective breeding of scallops in aquaculture.