Gene therapy has been extensively investigated and widely used in biomedical fields, such as cancer treatment. However, the most important issues for gene therapy are stability, targeting effect, transfection efficacy, and safety of gene formulation after administration, which seriously limit the further application of gene therapy in clinic. Therefore, gene delivery could be a promising strategy for overcoming these challenges. Two-dimensional (2D) materials are rising nanomaterials with excellent physical and chemical properties, including large specific surface area, easy modification, high conversion efficiency of light, and good biocompatibility, which have achieved promising applications as vehicles for gene delivery in the disease treatment. In this review, we first summarized the research progress of 2D material-based nanosystems for gene delivery to improve the therapeutic efficacy. We discussed that 2D material-based gene delivery nanosystems showed high therapeutic efficacy for many diseases treatment, especially cancer. Furthermore, we also proposed that surface modification of 2D materials might be a promising strategy to prepare multi-functional gene carriers for combination therapy with enhanced treatment efficacy. Finally, the future research progress, challenges, and prospects of 2D material-based nanosystems for gene therapy were discussed and concluded. Conclusively, we believe that 2D material-based nanosystems with good biocompatibility and high transfection efficiency would be potentially used in clinical settings to improve the therapeutic efficacy of gene therapy.