Once articular cartilage is damaged, it has poor ability to heal. At present, alginate-based hydrogels have 3D-dimensional physical structures with great potential for applications in carilage tissue engineering. For osteochondral defect, it will be necessary to use stratified scaffold to mimic zonal organization of cartilage. This study aims to compare the characteristics of alginate (Alg)/hyaluronic acid (HA) hydrogels which will mimic cartilage with alginate (Alg)/hydroxyapatite (Hap) hydrogels which will mimic subchondral bone. In this work, we fabricated the 3D-Alg/HA and Alg/Hap hydrogel scaffolds by the original spraying method. From the physical-mechanical properties, we compared mechanical behaviour of Alg/HA and Alg/Hap hydrogel scaffolds, which were examined using indentation testing and viscosity behaviour. This results showed that the Alg/Hap hydrogels exhibited a relative high mechanical strength, as well as the viscosity of Alg/Hap hydrogels is slight slower than Alg/HA hydrogels. However, autoclaving has more deleterious effect on the mechanical and viscosity properties of Alg/HA and Alg/Hap hydrogels. Cytotoxicity was evaluated through the culture of hydrogel beads-laden Wharton's jelly mesenchymal stem cells (WJ-MSC). In addition, the chondrogenic differentiation of WJ-MSC encapsulated into Alg/HA and Alg/Hap hydrogels were performed by histological analyzing during 30 days of culture. From these results, the percentage of living cells for Alg/Hap is significantly higher than Alg/HA, which also is associated with the results of shear viscosity. Both of hydrogels exhibited differentiate into chondrocyte matrix as collagen and proteoglycans. In conclusion, Alg/Hap hydrogels presented better mechanical property, cytocompatibility and differentiation characteristics than Alg/HA hydrogels.