The physicochemical properties and microstructure of hybrid hydrogels prepared using sodium alginate (SA) and chondroitin sulfate (CS) extracted from two animal sources were investigated. SA-based hybrid hydrogels were prepared by mixing chicken- and bovine-derived CS (CCS and BCS, respectively) with SA at 1/3 and 2/3 (w/w) ratios. The results indicated that the evaporation water loss rate of the hybrid hydrogels increased significantly upon the addition of CS, whereas CCS/SA (2/3) easily absorbed moisture from the environment. The thermal stability of the BCS/SA (1/3) hybrid hydrogel was higher than that of CCS/SA (1/3) hybrid hydrogel, whereas the hardness and adhesiveness of the CCS/SA (1/3) hybrid hydrogel were lower and higher, respectively, than those of the BCS/SA (1/3) hybrid hydrogel. Low-field nuclear magnetic resonance experiments demonstrated that the immobilized water content of the CCS/SA (1/3) hybrid hydrogel was higher than that of the BCS/SA (1/3) hybrid hydrogel. FTIR showed that S=O characteristic absorption peak intensity of BCS/SA (2/3) was obviously higher, suggesting that BCS possessed more sulfuric acid groups than CCS. SEM showed that the hybrid hydrogels containing CCS have more compact porous microstructure and better interfacial compatibility compared to BCS.