Stem cells self-renew, undergo multidirectional differentiation, and have great therapeutic potential for diabetes, brain injury, and acute myocardial infarction as examples. There are many types of stem cell products and many variations among batches. Therefore, quality control is particularly important for stem cell products before clinical use. Stem cells are immunogenic as living exogenous cells, and immunodeficient and humanized mice play an important role in stem cell quality control. Here, we review stem cell immunogenicities, summarize the commonly used immunodeficient and humanized mice, and outline the model applications of stem cell quality control to provide for a reference for stem cell quality control.