Regulatory T (Treg) cell dysfunction is involved in the pathogenesis of autoimmune premature ovarian insufficiency (POI). Adoptive transfer of Treg cells has been shown to be effective in the treatment of autoimmune POI in mice. However, the therapeutic effect of Treg cell therapy is limited because the phenotype and function of Treg cells is not properly maintained when they are reinfused in an inflammatory environment. Therefore, enhancing the function of Treg cells using genetic engineering is of great significance for improving the efficacy of Treg cells in the treatment of immune diseases. In this study, we investigated the role of the E3 ubiquitinated ligase Pellino 1 (Peli1) in the proliferation and immunosuppressive function of Treg cells and the therapeutic effect of Treg cells overexpressing Peli1 on autoimmune POI. The results showed that the overexpression of Peli1 promoted cell proliferation and enhanced the immunosuppressive function of Treg cells in vitro. After the adoptive transfer of Treg cells overexpressing Peli1 in autoimmune POI mice, the apoptosis rate of ovarian granulosa cells declined. The levels of the inflammatory inhibitors interleukin 10 and transforming growth factor-β as well as the ovarian hormone estradiol were elevated. The number of primordial, primary, secondary, and mature follicles was restored to a certain extent compared with those in control subjects. These results revealed that the adoptive transfer of Treg cells overexpressing Peli1 promoted its efficacy against zona pellucida protein 3 peptide-induced POI, which provides new insights into the treatment of autoimmune POI.