The present study was performed to explore the underlying molecular mechanism of Cu-induced disorder of lipid metabolism in fish. To this end, adult zebrafish were exposed to three waterborne Cu concentrations (0 (control), 8 and 16 μg Cu/L, respectively) for 60 days. Hepatic Cu content and hepatosomatic index increased after waterborne Cu exposure. H&E and oil red O stainings showed extensive steatosis in the liver of Cu-exposed fish. Cu exposure up-regulated lipogenic enzymes activities of ME, ICDH, 6PGD, G6PD and FAS, but down-regulated CPTI activities. Transcriptomic analysis indicated that lipid metabolism related pathways were significantly enriched in both low-dose and high-dose Cu exposure group. Genes involved in lipogenic process from fatty acid biosynthesis, fatty acid elongation, fatty acid desaturation to glycerolipid biosynthesis were up-regulated by Cu. To elucidate the mechanism, LXRα inhibitor SR9243 and SREBP1 inhibitor fatostatin were used to verify the role of LXRα and SREBP1 in Cu-induced disorder of lipid metabolism. Both SR9243 and fatostatin significantly attenuated the Cu-induced increase of TG accumulation of hepatocytes. Meanwhile, SR9243 significantly attenuated the Cu-induced up-regulation of expression of lipogenic genes (acaca, fas, icdh, dgat1, moat2 and moat3), and fatostatin significantly attenuated the up-regulation of expression of acaca, fas, g6pd, dgat1 and moat2. Enzymes analysis showed both SR9243 and fatostatin blocked the Cu-induced increase of lipogenic enzymes activities. Taken together, our findings highlight the importance of LXRα and SREBP1 in Cu-induced hepatic lipid deposition, which proposed a novel mechanism for elucidating metal element exposure inducing the disorder of lipid metabolism in aquatic vertebrates. •Hepatic Cu content and hepatosomatic index increased after waterborne Cu exposure.•Cu exposure induced extensive steatosis in the liver.•Cu altered the expression of genes related to lipogenesis and lipolysis.•LXRα and SREBP1 mediated Cu-induced hepatic lipid deposition.