10–23 DNAzyme (DrzBC) could block the expression of HBV e-gene with application limit of dependence on exogenous delivery. Stearic acid grafted chitosan oligosaccharide (CSSA) could self-aggregate to form micelles in aqueous medium and bind with DrzBC by electrostatic interaction. Compared with Lipofectamine™ 2000, the CSSA micelles showed much lower cytotoxicity (412.5 μg/mL) and advantaged target in subcellular organelles-cytoplasm. Both including DrzBC of 1 μmol/L, Lipofectamine™ 2000/DrzBC complex showed maximum inhibition rate (IR) on HBeAg expression of 46.53 ± 2.00% at 48 h, and then decreased rapidly, while CSSA/DrzBC complex showed maximum IR of 82.51 ± 1.28% at 72 h, and hold on IR above 70% until 96 h. Moreover, within a concentration range of 0.1–2.0 μmol/L, and equally incubating for 48 h, the IR of Lipofectamine™ 2000/DrzBC complex was from 23.20 ± 1.61% to 66.27 ± 1.96%, while the IR of CSSA/DrzBC complex increased from 40.23 ± 3.28% to 80.95 ± 1.69%. CSSA/DrzBC complex is a promising effective system for inhibiting HBeAg expression.