DNAzymes have the potential to suppress gene expression through sequence-specific mRNA cleavage and can therefore play an important role in various gene therapies. Hepatitis B virus (HBV) is still one of the most serious liver infections in people around the world and is difficult to treat. We previously designed a 10-23 DNAzyme called DrzBS, which targets HBV S gene expression, but this enzyme depends on exogenous delivery, and so its application has been limited. To overcome this limitation, we have now developed a chitosan-based nanocarrier (chitosan-g-stearic acid, CSO–SA) for intracellular delivery of DrzBS, then compared the inhibition effect of our CSO–SA/DrzBS complex to a common transfection reagent, Lipofectamine™ 2000/DrzBS, on hepatitis B surface antigen expression. The synthesized CSO–SA assembles into micelles in an aqueous solution and exhibits excellent cytoplasmic targeting, and could protect DrzBS from degradation by ribonuclease. CSO–SA/DrzBS showed a higher inhibition rate (IR) than Lipofectamine™ 2000/DrzBS. Moreover, at the same DrzBS concentration (1.2 μmol L−1), the maximum IR of CSO–SA/DrzBS micelles was 2.4-fold that of the Lipofectamine™ 2000/DrzBS complex, and held on for 96 hours. Compared with Lipofectamine™ 2000/DrzBS, CSO–SA/DrzBS achieved a higher HBV inhibition effect. This study demonstrates that CSO–SA micelles can serve as a potential vector for DrzBS and that CSO–SA/DrzBS micelles are a promising application for anti-HBV gene therapy.