Polyunsaturated fatty acids (PUFAs) promoted the muscle structure (muscle fiber cross-sectional area and diameter, as well as thickness of the connective tissue surrounding muscle fibers-endomysium) and taste (fishy) of fillets. As members of the omega-3 and omega-6 PUFA family, alpha-linolenic acid (ALA) and linoleic acid (LNA) have important functions. This study explores influences of ALA/LNA ratio on muscle growth and protein deposition and its mechanisms. Six different diets containing ALA/LNA ratios (0.03, 0.47, 0.92, 1.33, 1.69, and 2.15) were fed to grass carp (Ctenopharyngodon idella) for 9 weeks. Results showed that according to the quadratic regression model, the optimal ALA/LNA ratios of grass carp were 1.12 and 1.22 using malondialdehyde content and muscle fiber diameter as indicators, respectively. Optimum ALA/LNA ratio promoted hypertrophy of myofibers, which might be attributed to genes related to myofiber development (myogenic determinant, myogenin, myosin heavy chain, myogenic regulatory factor 4 and myogenic factor 5). Optimum ALA/LNA ratio enhanced protein deposition, which might be associated with the promotion of protein synthesis (insulin-like growth factors-1, phosphoinositide 3-kinase, target of rapamycin), and inhibition of the ubiquitin-proteasome system and autophagy-lysosome system to inhibit protein degradation. In addition, optimum ALA/LNA ratio enhanced muscle amino acid composition and antioxidant capacity of fish.