Background: Fatty acid (FA) consumption can alter hepatic energy metabolism and liver mitochondrial functions. Crocodile oil (CO) is rich in both mono- and polyunsaturated fatty acids that contain natural anti-inflammatory and healing properties. We investigated the effect of CO on energy metabolism and mitochondrial morphology in rat liver.Methods: Twenty-one male Sprague–Dawley rats were randomly divided into three groups. Group 1: rats treated with sterile water (RO); group 2: rats treated with CO (3% v/w); and group 3: rats treated with palm oil (PO) (3 % v/w). Rats were orally administered sterile water, CO, and PO once daily for 7 weeks. Body weight, food intake, liver weight, energy intake, blood lipid profiles, and liver-targeted metabolites were evaluated. Histopathological study of the liver, mitochondrial architecture of liver cell, and HDHD3 protein expression in liver mitochondria were determined.Results: CO treatment had no effect on body weight, liver weight, liver index, dietary energy intake, and serum lipid profiles. The CO group exhibited significantly lower food intake than the RO group. The CO group also showed significantly higher oxaloacetate and malate levels, which encourage the TCA cycle imbalance, than the PO group. CO treatment significantly ameliorated hepatic steatosis as shown by a greater decrease of total surface area of lipid particles than that seen with PO treatment. CO administration maintained the liver’s mitochondrial morphology by upregulating the energetic maintenance protein—HDHD3. Moreover, the chemical-protein interaction also showed that the main fatty acid composition of CO preserved liver metabolism via the AMPK signaling pathway.Conclusion: Crocodile oil could support hepatic function through promoting the TCA cycle, maintaining hepatic mitochondrial architecture, and upregulating HDHD3.