Objective This study aims to investigate the regulatory effects of microcapsules with different matrix stiffness on the survival, proliferation, adhesion, and osteogenic differentiation of mesenchymal stem cells (MSCs), to further explore the relationship between matrix stiffness and MSCs osteogenic behavior, and to evaluate the in vivo histological responses and osteogenic-related protein expression of the microcapsules using an animal subcutaneous implantation model.Methods In this study, three-dimensional carbon nanofiber (CNF)/sodium alginate (SA) microcapsules with different matrix stiffness were constructed. By adjusting the CNF content, three groups of microcapsules with stiffness values of 27.05, 35.90, and 52.40 kPa were prepared, and their physicochemical properties, including morphology, mechanical properties, particle size, chemical structure, and degradation properties, were characterized. The effects of these microcapsules with different stiffness on the survival, adhesion, and osteogenic differentiation of MSCs were evaluated. Live/dead staining was used to observe cell survival and distribution in the microcapsules, while alkaline phosphatase (ALP) activity and the expression of osteopontin (OPN) and osteocalcin (OCN) were examined to assess osteogenic differentiation. Immunofluorescence staining was further performed to observe the expression of Yes-associated protein (YAP) and integrin β1 under different stiffness conditions. In addition, a rat subcutaneous implantation model was used to evaluate the in vivo tissue compatibility of the microcapsules. Histological staining and immunohistochemical analysis were carried out to examine local tissue responses and the expression of osteogenic-related proteins.Results The results showed that all three groups of microcapsules exhibited regular and uniform morphology and similar particle size, and all groups showed good degradability. Except for the differences in mechanical properties, no obvious differences were found in the other physicochemical properties among the three groups. Live/dead staining indicated that all groups of microcapsules had good cytocompatibility. MSCs in the low-stiffness group were mostly round, whereas cells in the medium- and high-stiffness groups showed more obvious spreading. Higher matrix stiffness was more favorable for MSC adhesion, growth, and survival. ALP staining and quantitative analysis showed that ALP activity increased significantly with increasing matrix stiffness. The expression of the osteogenic-related proteins OPN and OCN also increased with increasing stiffness, and the high-stiffness group showed the strongest positive signals. Immunofluorescence results further indicated that YAP and integrin β1 fluorescence signals tended to increase in MSCs with increasing matrix stiffness, suggesting that matrix stiffness may influence MSC osteogenic differentiation through stiffness-related cell adhesion and mechanotransduction. In vivo experiments showed that all three groups of microcapsules exhibited good histocompatibility after subcutaneous implantation, although different degrees of degradation and local tissue response were observed. Immunohistochemical analysis showed that the expression levels of OPN and OCN increased with increasing matrix stiffness, and the high-stiffness group exhibited higher expression of these osteogenic-related proteins.Conclusion CNF endows SA microcapsules with tunable matrix stiffness. While maintaining good biocompatibility, the high-stiffness microenvironment can effectively promote the adhesion and osteogenic differentiation of MSCs, accompanied by increased ALP activity and enhanced OPN and OCN expression. The increased YAP and integrin β1 fluorescence signals in the high-stiffness group further indicate that matrix stiffness is closely related to cellular mechanical responses. These findings provide a three-dimensional cell carrier with potential application value for MSC delivery and bone tissue regeneration based on mechanical microenvironment regulation.