Background: The uterine endometrium plays a important role in the processes of fertilization and embryogenesis, with its impairment or dysfunction leading to pathologies such as intrauterine adhesions, miscarriage, and infertility. In addressing endometrial damage, the application of stem cell has attracted considerable attention. To promote the paracrine capabilities of mesenchymal stem cells (MSCs), this study employed pro-inflammatory cytokines (Tumor Necrosis Factor-α and Interferon-γ, TNF-α and IFN-γ, IT) along with 3D culture techniques on pretreated MSCs (3D-IT-MSCs). We focused on evaluating the therapeutic potential of 3D-IT-MSCs and elucidating the mechanisms involved in endometrial repair. Method: Pretreated MSCs were co-cultured with human umbilical vein endothelial cells (HUVECs) or drug-induced endometrial stromal cells (ESCs) to observe the promoting effect on biological function. Results: The findings demonstrated that 3D-IT-MSCs exhibit markedly elevated paracrine molecule expression and secretion compared to conventional MSCs. Additionally, treatment with 3D-IT-MSCs significantly promoted the proliferation and migration of HUVECs and ESCs, resulting in increased HUVECs angiogenesis and inhibition of mifepristone-induced ESCs apoptosis. Conclusion: Our findings demonstrated that the combined approach of applying pro-inflammatory cytokines and 3D culture techniques on pretreated MSCs holds substantial promise as a therapeutic strategy for repairing endometrial injuries.