Duck hepatitis A virus genotypes 3 (DHAV-3) has become the most prevalent pathogen of duck viral hepatitis (DVH) in Asian duck industry in recent years. Previous studies on the pathogenic mechanism of DHAV-3 mainly focused on examine host gene expression levels. However, the study about host protein expression levels has not been reported. For this, proteomics analysis on livers of infected 7-day-old Pekin ducks with DHAV-3 112803 strain was performed to screen differentially expressed proteins. A total of 3,385 proteins were identified, and we found 39 proteins in the challenged group (CH) were significantly up-regulated and 15 proteins were significantly down-regulated in comparison with control group (CON). GO results showed that 9 of the top 20 GO terms were involved in type I interferon regulation, and the KEGG pathway enrichment results showed that innate immune responses were significantly enriched, such as RIG-1-like, Toll-like and NOD-like receptor signaling pathways. Notably, interaction between 11 up-regulation proteins promoted interferon-induced protein synthesis and supported viral genome replication, which could aggravate inflammatory response and liver damage. These findings, together with RT-qPCR verification of related genes, support the view that the type I interferon may play an extremely important role in the pathogenic mechanism of DHAV-3.