The thymus is a key organ for the development and maturation of T cells, and its resection may have profound effects on the body’s immune function. Postoperative immune alterations may include reduced diversity of the T-cell repertoire, accelerated immune senescence, and dysfunction of regulatory T cells (Tregs). There may also be an increased long-term risk of infections, autoimmune diseases, and tumors. Furthermore, the immunological impact varies significantly among different populations and between partial and total thymectomy. Current research findings remain controversial, limited by factors such as substantial population heterogeneity and short follow-up periods. Future studies should involve multicenter, long-term, large-scale follow-up research. Additionally, individualized surgical and intervention strategies should be developed to improve the long-term prognosis of patients.