Abstract: To evaluate the effects of supplementation in high cottonseed and rapeseed meal diets on overwintering stress and post-winter refeeding in grass carp (Ctenopharyngodon idella), two consecutive feeding trials were conducted during the overwintering period (Experiment 1) and the recovery phase (Experiment 2). Experiment 1 included a pre-overwintering control (CON), a post-overwintering control (HCON), a high cottonseed and rapeseed meal diet group (HCA0), and a diet supplemented with 0.15% Citrus aurantium extract (HCA1). Experiment 2 involved refeeding for 2 weeks with a cottonseed meal diet (FCA0) or diets supplemented with 0.15% (FCA1) or 0.5% (FCA2) extract. The results demonstrated that overwintering stress significantly triggered intestinal physiological dysfunction in grass carp, primarily characterized by suppressed digestive enzyme activities (amylase, lipase, and trypsin), tight junction dysregulation (zo-1 and cl-b/c downregulation; cl-12/15 and mlck upregulation), alongside severe hepato-intestinal architectural disruption and altered serum biochemical profiles (elevated AST/ALT; diminished TG/TC). Concurrently, overwintering stress suppressed the Nrf2/Keap1 antioxidant signaling pathway (nrf2, cat, CuZnsod, gpx1, and gr downregulation; keap1 upregulation), while activating NF-κB–mediated inflammatory responses (tnf-α and il-8 upregulation; il-15 and tgf-β1 downregulation). The HCA0 group showed the most severe impairment, whereas the HCA1 group maintained physiological indices comparable to the CON group. Post-refeeding, CAE exhibited a dose-dependent recovery, with the 0.5% dose (FCA2) most effectively restoring enzymatic activity, physical barrier integrity, and antioxidant/immune status. Collectively, dietary CAE alleviates cold-induced hepato-intestinal injury by preserving digestive enzyme function and coordinately regulating oxidative stress and immune responses, thereby maintaining physiological homeostasis in overwintering grass carp fed high cottonseed and rapeseed meal diets and conferring pronounced protective effects during short-term refeeding.