Background: Environmental disorders of the circadian rhythms can lead to metabolism-related diseases or exacerbate pathological conditions. Non-alcoholic fatty liver disease (NAFLD) has emerged with a growing occurrence. In the present study, we attempted to indicate whether circadian clock may influence lipid deposition and the expression levels of autophagy-related genes in liver of mice. Methods: High-fat diet and abnormal light/dark cycles were employed to induce a mouse model of NAFLD with circadian rhythm sleep disorder. Herein, liver samples were obtained at ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20 time-point to detect the rhythmic expressions of circadian genes, autophagy-related genes, and Rev-erbα. Results: Abnormal exposure to light aggravated lipid deposition in liver of mice and exacerbated disorders related to 24-h expression levels of clock genes, autophagy-related genes, and Rev-erbα. Besides, Rev-erbα could transcriptionally control the expression levels of autophagy-related genes. Conclusions: The long-term high-fat diet combined with abnormal light/dark cycle stimulation aggravated the development of NAFLD and disturbed the expressions levels of autophagy-related genes. An abnormal circadian expression may lead to NAFLD aggression. Besides, the abnormal expression levels of clock genes may create an association between circadian rhythm sleep disorder and autophagy.