Previous studies have demonstrated that single nucleotide polymorphisms (SNPs) rs12427129 and rs3816153 in HOX transcript antisense intergenic RNA (HOTAIR) might interact with hepatitis B virus (HBV) infection to increase the risk of hepatocellular carcinoma (HCC). However, it is unclear whether HBV infection is a potential mediator between HOTAIR rs12427129, rs3816153, and HCC. This study, including 1262 HCC cases and 1559 controls, aimed to use a four-way decomposition method to quantify the interaction and mediation effects of HBV infection in the association between rs12427129, rs3816153, and HCC. We found that rs12427129 and rs3816153 were associated with a risk of HBV infection among the controls (CC: CT+TT, adjusted odds ratio (OR)=1.77, 95% confidence interval (CI)=1.32-2.36 and GG: GT+TT, adjusted OR=0.63, 95% CI=0.48-0.82). The four-way decomposition revealed that rs12427129, rs3816153, and HBV infection had statistically significant reference interaction on HCC (excess risk (95% CI): -0.362 (-0.530, -0.195), p<0.001 and excess risk (95% CI): 0.433 (0.059, 0.808), p=0.023), and the proportion attributed to reference interaction were 110.82% and 125.27%, respectively. The pure indirect effect suggested that the rs3816153 GT + TT genotype can reduce the risk of HCC by 21.79% (excess risk (95% CI): -0.075 (-0.142, -0.009), p=0.026) when HBV infection as a mediator. Our findings suggested that HBV infection interacts or mediates with the association between rs12427129, rs3816153, and HCC. This would provide a new perspective for exploring the underlying biological mechanism between HOTAIR SNPs, HBV infection, and HCC.