As a major therapy for hepatitis B virus (HBV) infection, Interferon alpha (IFN-alpha) triggers intracellular signal transduction including JAK-STAT pathway to produce various antiviral effector mechanisms. However, patients with chronic hepatitis B usually show low response to IFN-alpha treatment and the underlying mechanism remains unclear. In the present study, HepG2 and HepG2.2.15 cells were used to examine the Type I IFN receptors expression, phosphorylation and methylation of STAT1. STAT1-PIAS1 interaction in cells was tested by protein co-immunoprecipitation. The potential improvement of S-adenosylmethionine (SAM) in the antiviral effect of IFN-alpha was also investigated. Our data demonstrated that both chains of the Type I IFN receptors were expressed for a much higher extent in HepG2.2.15 cells than in HepG2 cells. HBV inhibited dramatically the methylation rather than the phosphorylation of STAT1, which was consistent with an increased STAT1-PIAS1 interaction. Combined with IFN-alpha, SAM treatment effectively improved STAT1 methylation and attenuated STAT1-PIAS1 binding, followed by increased PKR and 2',5'-OAS mRNA expression, thus significantly reducing the HBsAg, HBeAg protein levels and HBV DNA load in the supernatant of HepG2.2.15 cells. Less STAT1 methylation and subsequent increased STAT1-PIAS1 interaction are involved in the mechanism of the IFN-alpha-antagonistic activity of HBV. By improving STAT1 methylation, SAM can enhance the antiviral effect of IFN-alpha.