Senile thymus atrophy is an important factor leading to decreased immune function. Repairing the atrophic thymus tissue structure, rebuilding immune function, and replenishing the number of exogenous stem cells may be effective methods. In this study, BMSCs (Bone Marrow Mesenchymal Stem Cells, BMSCs) were intravenously infused into elderly macaques. We found that thymus area was substantially increased, some thymus tissue regeneration was observed, the degree of thymus tissue fibrosis decreased, collagen fibre deposition decreased, cortical and medulla structures emerge gradually, the number of apoptotic cells decreased significantly, inhibit the expression of apoptosis-related proteins. Bone marrow mesenchymal cells inhibit the expression of genes related to aging. By sequencing the mRNA transcriptome in thymus tissue, the expression pattern of the tissue transcriptome tended to be similar to the thymus expression pattern in young macaques compared with the old group, reverse aging-related proteins. Based on the results, an intravenous infusion designed to increase the number of stem cells in the body effectively repairs the structure of the thymus and rebuilds immune function.