Background: Chronic hepatitis B virus (CHBV) infection is a major cause of liver diseases. Mucosal-associated invariant T (MAIT) cells are important for antiviral immunity in the liver, but the distinction between intrasinusoidal MAIT cells and peripheral MAIT cells in patients with CHBV infection remains unclear. Methods: PBMC were obtained from patients with CHBV infection (n=51) and age-matched controls (n=52). Liver-associated mononuclear cells (LMCs) were collected from donors (n=32) and explanted liver (n=23) of patients to perform phenotypic, functional and TCR diversity analysis. Results: The frequency of intrasinusoidal MAIT cells in the CHBV infection group was not changed compared to that of the MAIT cells in the CHBV-negative group. However, the frequency of peripheral blood MAIT cells was severely reduced in the CHBV infection group compared to the CHBV-negative group. Moreover, IFN-γ production was intact in the intrahepatic MAIT cells of the CHBV infection patients compared to those of the control subjects post IL-12 and IL-18 stimulation, while it was reduced in the peripheral blood MAIT cells of the CHBV infection patients. More importantly, our study showed that the expression level of HLA-DR in peripheral MAIT cells was higher than that in intrasinusoidal MAIT cells in CHBV infection patients. A distinct signature of TCR usage was found in the CHBV patients. Conclusions: By analysing the phenotype, function and TCR usage of MAIT cells in the PBMC and LMC populations of patients with CHBV infection, we found distinct functions and activities in the MAIT cells of the liver compared with those of the peripheral blood. Funding Statement: YG is supported by Natural Science Foundation of Guangdong Province (Grant number: 2018A030313019) and National Natural Science Foundation of China (Grant number:31800758). Declaration of Interests: All authors disclose no conflicts of interest. Ethics Approval Statement: This study was fully approved by the First Affiliated Hospital of Sun Yat-sen University ethical board. All participants provided written informed consent before sample collection.