As the seed cells, the immune properties of the mesenchymal stem cells are important for the tissue engineering restoring effect. But the in vivo research model is lacking. In the study, based on a dialyzer pocket model, changes in immunological properties and the differentiation of seeded mesenchymal stem cells (MSCs) in collagen hydrogel were studied in muscle and articular cavity implantation, respectively. The results showed that collagen hydrogel can induce MSCs to form cartilage tissue, followed by alteration of immunological properties. In muscle implantation, relatively low expression of major histocompatibility complex (MHC) molecules and low level of one-way mixed lymphocyte reactions (MLR) on the seeded MSCs were observed, but only a little cartilage tissue formed. In articular cavity implantation, more cartilage tissue formed, but higher MHC expressions and MLR level were found. Results indicated that the immunomodulation and the cartilage formation of the seeded MSCs will be impacted by the scaffold and the environment of the in vivo implanted site. The dialyzer pocket model can be used for the in vivo research for the MSC-based strategy of the tissue engineering, especially for the optimization of the immunomodulation.