Nobiletin (NOB), a naturally occurring small-molecule compound abundant in citrus peels, has displayed potential lipid-lowering and circadian-enhancing properties in preclinical studies. However, the requirement of specific clock genes for the beneficial effects of NOB is not well understood. In the current study, mice with a liver-specific deletion of the core clock component,Bmal1—Bmal1LKO—were fed a high-fat diet (HFD) ad libitum for eight weeks, while NOB (200 mg/kg) was administered by daily oral gavage from the fifth week and throughout the last four weeks. NOB decreased liver triglyceride (TG) alongside the decreasing mRNA levels of de novo lipogenesis (DNL) genes in bothBmal1flox/floxandBmal1LKO mice. NOB increased serum very low-density lipoprotein (VLDL) levels inBmal1LKO mice, which was consistent with higher liverShpand lowerMttpmRNA expression levels, the key genes that facilitate VLDL assembly and secretion. NOB decreased liver and serum cholesterol levels in theBmal1flox/floxmice, consistent with lowerHmgcrand higherCyp7a1,Cyp8b1,Gata4andAbcg5mRNA levels in the liver. In contrast, in theBmal1LKO mice, NOB increasedHmgcrmRNA levels and had no effect on the above-mentioned genes related to bile acid synthesis and cholesterol excretion, which might contribute to the elevation of liver and serum cholesterol levels in NOB-treatedBmal1LKO mice. NOB inhibited hepatic DNL and decreased liver TG levels in HFD-fed mice independently of liverBmal1, whereas liver-specificBmal1depletion reversed the beneficial effects of NOB on liver cholesterol homeostasis. The complex interactions between NOB, the circadian clock and lipid metabolism in the liver warrant further research.