Zwitterionic sulfobetaine (SB) and carboxybetaine (CB) have been extensively investigated for their noticeable antifouling properties. Both SB and CB have cationic and anionic groups in the molecule, but they differ in negatively charged groups. Molecular simulations have been conducted to investigate the different properties induced by structure changes. However, few studies have focused on the differences between SB and CB materials, especially zwitterionic polysaccharides. Two zwitterionic sulfobetaine and carboxybetaine dextran hydrogels were designed and used as models to compare their properties. Results showed that the equilibrium swelling ratios of the SB-DEX hydrogels were much higher than CB-DEX ones, and larger interior pores were observed in the SB-DEX hydrogels due to their higher hydrophilicity. The rheological storage modulus of the SB-DEX hydrogels was lower than that of CB-DEX ones as a result of higher water content of SB-DEX. These results were consistent with molecular modeling. Additionally, both CB-DEX and SB-DEX had remarkable biocompatibilities, and the in vitro release studies showed that the SB-DEX and CB-DEX hydrogels released DOX in a sustained manner under acidic condition (pH 5.0), indicating their promise as an effective drug-delivery system.