Chronic hepatitis B virus (HBV) infection causes hepatitis, liver cirrhosis and hepatocellular carcinoma. Covalently closed circular DNA (cccDNA) is the transcription template for HBV RNAs and not affected by current treatment options. Effective therapeutics with ability to remove cccDNA need to be developed. Previously, we established an HBV persistence mouse model via hydrodynamic injection of a clinical isolate (BPS) and identified IL-21 as a potent inducer of viral clearance. Here, we aimed to explore the anti-HBV effects of IL-21 messenger RNA (mRNA) delivered by lipid nanoparticle (LNP-IL-21) system. First, LNP-IL-21 was prepared and analyzed for its safety, expression, biodistribution and stability in vitro and in vivo. Next, LNP-IL-21 was injected into two HBV persistence mouse models based on BPS and recombinant cccDNA (rcccDNA) respectively. LNP-IL-21 administration successfully cleared HBV serum markers, and more importantly, BPS replicons and rcccDNA in livers, which was associated with activation of viral specific immune responses. Notably, transfer of peripheral blood mononuclear cells from BPS persistence mice stimulated ex vivo with LNP-IL-21 and viral antigen could induce HBV clearance in recipient mice. These findings suggested that both LNP-IL-21-based gene and cellular therapies provided novel therapeutic strategies against chronic HBV infection.