Organ transplantation is the ultimate treatment for end-stage diseases such as heart and liver failure. However, the severe shortage of donor organs has limited the organ transplantation progress. Xenogeneic stem cell transplantation provides a new strategy to solve this problem. Researchers have shown that xenogeneic stem cell transplantation has significant therapeutic effects and broad application prospects in treating liver failure, myocardial infarction, advanced type 1 diabetes mellitus, myelosuppression, and other end-stage diseases by replacing the dysfunctional cells directly or improving the endogenous regenerative milieu. In this review, the sources, problems and solutions, and potential clinical applications of xenogeneic stem cell transplantation will be discussed.