Two-dimensional (2D) transition metal carbides and/or nitrides (MXenes), promising electrode materials for Li-ion batteries (LIBs), have recently been confirmed the formation of vacancies during etching process. However, the specific influence of vacancies on the performance of MXene-based LIBs and the corresponding mechanism still remain open issues. Herein, we highlighted that compared with other well-studied 2D materials (such as graphene, 2D MoS2), MXene are more likely to contain vacancies with defect formation energies as low as 0.96 eV. The difference of vacancy formation energy for MXenes mainly originates from the variation of M-X bonding strengths. Furthermore, the vacancy defect will enhance the adsorption of Li in the region near the defect through acting as a potential trap, which may cause the first cycle irreversibility for lithiation/delithiation process in Mo2C MXene LIBs. Nevertheless, Li tends to migrate on defect-free surface of Mo2C MXene with energy barrier of 0.096-0.115 eV and thus this potential trap has a minor influence on the charge-discharge rate of Mo2C MXene LIBs. We believe that our findings provide not only some insights into the recent experimental results but also guidance for the preparation and practical application of MXene in LIBs.