Methotrexate (MTX) is the most common therapeutic agent that may have the risk of drug-induced liver injury. Its pathogenic mechanism is related to oxidative stress caused by mitochondrial dysfunction. Superoxide dismutase (SOD), including manganese-containing SOD (Mn-SOD), can exert its effect of anti-oxidative stress by scavenging superoxide free radicals. Accordingly, this study is performed to explore the underlying molecular mechanism via observing whether Mn-SOD could affect the damage of MTX to hepatocytes. Human hepatocyte cell line L-02 was cultured in vitro and divided into 4 groups, including a blank group with the addition of the same volume of serum-free medium, a MTX group (40 μg/well MTX drug-treatment), a MTX+NC group (40 μg/well MTX drug-treatment+blank plasmid), and a MTX+SOD group (40 μg/well MTX drug-treatment+Mn-SOD plasmid). The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and microRNA-122 (miR-122) in the supernatant of cell culture were respectively detected by automatic biochemical analytical instrument and real-time RT-PCR to evaluate the degree of hepatocyte damage in each group. MitoSOX fluorescent probe was used to label intracellular superoxide in each group, and cell apoptosis was detected by flow cytometry. Meanwhile, the contents of glycogen synthase kinase-3 beta (GSK-3β), hemeoxygenase-1 (HO-1), mitochondrial fission-mediated protein of dynamin-related protein 1 (Drp1), and Mn-SOD were detected by Western blotting. Compared with the blank group, the levels of ALT, AST, and miR-122 in the supernatant of hepatocyte culture of the MTX group and MTX+NC group were significantly elevated (all P <0.05), and that in the MTX+SOD group were significantly decreased ( P <0.05) and equivalent to that in the blank group. MitoSOX staining revealed that the MTX group and MTX+NC had the most abundant superoxide; and the amount was significantly reduced in the MTX+SOD group, without a significant difference when compared with the blank group. Furthermore, the results of flow cytometry indicated that compared with the blank group, the MTX group and MTX+NC group showed significantly increased cell apoptosis ( P <0.05); while there was obviously reduced cell apoptosis in the MTX+SOD group than that in the MTX group and MTX+NC group ( P <0.05). According to the results of Western blotting, the blank group and MTX+SOD group had higher expressions of Mn-SOD, p-GSK-3β, and HO-1; while the MTX group and MTX+NC group exhibited remarkably lower levels of Mn-SOD, p-GSK-3β, and HO-1 than those in the blank group ( P <0.05). Besides, a completely opposite trend was found in the expression of Drp1, which was highly expressed in the MTX group and MTX+NC group, but lowly expressed in the blank group and the MTX+SOD group. MTX may induce hepatocyte damage, and one of the mechanisms may be due to the decrease of intracellular Mn-SOD level, which can cause the accumulation of superoxide, affect the levels of HO-1 and Drp1 through GSK-3β leading to mitochondrial damage and cell apoptosis. High expression of Mn-SOD intracellularly through exogenous introduction can scavenge drug-produced superoxide, affect HO-1 and Drp1 levels through GSK-3β, activate mitochondria, protect cells against damage from oxidative stress, and inhibit hepatocyte apoptosis eventually. So exogenous introduction of SOD may be a potential therapeutic approach to block or reverse MTX-related hepatocyte injury.