For alcoholic liver disease (ALD), mitophagy has been reported as a promising therapeutic strategy to alleviate the hepatic lesion elicited by ethanol. This study was conducted to investigate the regulatory effects of fucoidan on mitophagy induced by chronic ethanol administration in rats. Here, 20 male rats in each group were treated with fucoidan (150 and 300 mg per kg body weight) by gavage once daily. Up to 56% liquor (7 to 9 mL per kg body weight) was orally administered 1 h after the fucoidan treatment for 20 weeks. The results showed that chronic ethanol consumption elevated the levels of hepatic enzymes (ALT, AST, and GGT) and triglyceride (TG) contents, with liver antioxidant enzymes being decreased and lipid peroxidation products increased and thus initiating the mitochondria-induced endogenous apoptotic pathway. Furthermore, ethanol-induced excessive oxidative stress inhibited the function of mitochondria and promoted damaged mitochondria accumulation which stimulated the PTEN-induced putative kinase 1 (PINK1) and Parkin associated mitophagic pathway in the liver. In contrast, the fucoidan pretreatment alleviated ethanol-induced histopathological changes, disorders of lipid metabolism, and oxidative damage with mitophagy related proteins and mitochondrial dynamics-related proteins namely mitochondrial E3 ubiquitin ligase 1 (Mul1), mitofusin2 (Mfn2) and dynamin-related protein 1 (Drp1) being restored to a normal level. In summary, our findings suggest that fucoidan pretreatment protects against ethanol-induced damaged mitochondria accumulation and over-activated mitophagy, which plays a pivotal role in maintaining mitochondrial homeostasis and ensuring mitochondrial quality.