Chronic hepatis B with HDV (Hepatitis D Virus) coinfection is considered as one of the most serious forms of human viral hepatitis that can lead to cirrhosis and hepatocellular carcinoma. However, the high GC ratios in HDV genome and the same surface antigen protein HBsAg (Hepatitis B surface Antigen) in virus particles assembly make it hard (or ignored) to diagnose HDV co-infection with HBV (Hepatitis B Virus) using traditional methods (i.e., antibody-surface antigen reaction), further limit to build epidemiologic information on HDV. Thus, developing efficient detection for key pathogenetic molecules of HDV becomes key experimental questions for HDV diagnosis. In these key molecules, specific HDAgs (Hepatitis D Antigens, including large and small HDAgs) are the solitary ribonucleoproteins encoded by HDV genome, which function in viral life cycle in significant ways. Herein, we propose a direct and precise detection for large and small HDAgs using nanopore sensor in asymmetric ionic liquids electrolyte condition. What's as obvious from nanopore measurement for either antigen is that the results allow discriminate large and small HDAgs as well as antigen-ribozyme complex in serological assay. More importantly, it is ascertained by nanopore test that HDAgs can be efficiently distinguished with HBsAg in HBV-infected cells, enabling simultaneous identification of HBV- and HDV-infected cells. In conclusion, the proposed nanopore can provide specific and efficient detection of physiological indicators for different hepatitis virus infections at molecular and cellular levels, and should benefit severer HBV/HDV co-infection diagnosis and therapy.