BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to branched-chain amino acid (BCAA) dysmetabolism and ferroptosis, and exercise is considered protective, yet the underlying mechanisms remain unclear. METHODS: Integrated bioinformatic analyses of public datasets were performed to identify key regulators of MASLD. Hepatic inositol hexakisphosphate kinase 3 (IP6K3) expression was examined in liver samples from patients with MASLD as well as mice. The functional role of IP6K3 was assessed by either hepatocyte-specific Ip6k3 deletion or exercise intervention in mice. Single-cell RNA sequencing (scRNA-seq), IP6K3 overexpression and knockdown, liquid chromatography-tandem mass spectrometry, and co-immunoprecipitation were used to explore the underlying mechanism by which IP6K3 regulates MASLD. RESULTS: Hepatic IP6K3 was significantly upregulated in both patients with MASLD as well as mice, and exercise markedly attenuated hepatic IP6K3 expression in MASLD mice. Hepatocyte-specific Ip6k3 deletion conferred resistance to MASLD-induced liver injury. scRNA-seq revealed that these protective effects were related to enhanced BCAA degradation and inhibition of ferroptosis. Further studies showed that BCAA degradation was dependent on branched-chain aminotransferase 2 (BCAT2). In vitro, IP6K3 overexpression exacerbated BCAA-promoted ferroptosis, which was rescued by ferrostatin-1. Conversely, IP6K3 knockdown prevented ferroptosis, and this effect was abolished by inhibiting BCAT2. Mechanistically, elevated IP6K3 in MASLD could bind to heterogeneous nuclear ribonucleoprotein K (HNRNPK) in hepatocytes. Exercise-downregulated IP6K3 facilitated HNRNPK release, thereby stabilizing BCAT2 mRNA, promoting BCAA catabolism, and ultimately preventing ferroptosis in MASLD. CONCLUSIONS: Our study identifies IP6K3 as a key molecule in exercise-induced protection against MASLD, and suggests that IP6K3 inhibition might represent a potential pharmacological strategy for MASLD intervention.