Duck viral hepatitis (DVH) is a common and serious acute infectious disease that has a significantly impact on the duck farming industry. Duck hepatitis A virus type 3 (DHAV-3) is the major causative agent of DVH in East Asia. Host factor indicators of resistance to DHAV-3 in Pekin ducks were investigated using resistant (Z7R) and susceptible (Z7S) duck lines. Before DHAV-3 infection, Z7R had significantly higher HDL-C and LDL-C levels than Z7S. The results of population verification showed that Pekin ducks with HDL-C and/or LDL-C concentrations within their maximum 5 % confidence interval were highly resistant to DHAV-3. RNA-seq identified fifteen differentially expressed genes, primarily involved in lipid metabolism. Additionally, lipidomics identified one hundred distinct metabolites involved in glycerophospholipid metabolism. The ACSL6 gene was found to be significantly associated with PC and PE. ACSL6, PE, PC, HDL-C and LDL-C co-regulated hepatic lipid metabolism. In conclusion, our results reveal that HDL-C and LDL-C may serve as markers of anti-DHAV-3 infection and lipid metabolism may be related to a potential mechanism of antiviral activity in Pekin ducks, providing a theoretical basis for future studies on the interaction between lipid metabolism and DHAV-3.