Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian carp (HCC) using physiological and transcriptomic analyses. Fish were fed three diets for 8 weeks: a basal diet (LA) and two diets supplemented with DL-methionine at 1.7% (MA) and 3.4% (HA), respectively, while L-lysine supplementation was fixed at 3.4%. The results indicated that dietary Met and Lys supplementation had no significant effect on the growth performance of HCC (p > 0.05), but significantly reduced serum triglyceride (TG) and cholesterol levels (T-CHO) (p < 0.05). Additionally, serum total protein (TP) content was significantly increased in the MA group (p < 0.05). Analysis of serum antioxidant enzyme activities indicated that appropriate Met and Lys supplementation improved antioxidant capacity and upregulated the expression of antioxidant-related genes (Nrf2, GPX1a, GSTO1, GSTP1) in the muscle. Moreover, the MA group exhibited superior muscle hardness and gumminess, while the HA group had higher springiness and chewiness (p < 0.05). Muscle fiber density was significantly increased, whereas diameter and area showed opposite trends in fish fed 1.7% Met and 3.4% Lys (p < 0.05). Furthermore, appropriate Met and Lys supplementation significantly affected muscle fiber development genes (MyoD, MyoG, and MRF4), with MyoG highest in the HA group and MyoD and MRF4 highest in the MA group (p < 0.05). Comparative transcriptomic analysis of muscle tissue showed DEGs were mainly enriched in pathways correlated with muscle quality, involving cardiac muscle contraction, actin cytoskeleton regulation, PPAR signaling pathway and ECM–receptor interaction. Taken together, our findings enhance the understanding of the molecular mechanisms underlying the effects of dietary Met and Lys on muscle quality in HCC, providing valuable insights for the development of nutritional strategies in the aquaculture industry.