Long-term waterproofing and water leakage treatment of existing underground structures have become prominent issues in the operation and maintenance of underground structures. The use of single organic or inorganic materials for water leakage treatment is not effective for solving practical engineering problems. Considering the properties of organic and inorganic materials, a novel composite material mixing the waterborne epoxy resin and superfine ordinary Portland cement-sulphoaluminate cement was presented, which was studied as a polymer-modified cementitious composite for waterproofing and plugging. This study investigated the primary physical properties of the raw materials of the polymer-modified cementitious composite. Experimental tests were performed to investigate the effects of waterborne epoxy resin on the impermeability, interface adhesion, and tensile deformation performances of the superfine cementitious waterproof material. The results showed that the average water penetration height of the waterborne epoxy resin-modified material was only 52.2% that of the cementitious materials, indicating better impermeability performance. When 3% waterborne epoxy resin was mixed, the bending bond strength of the polymer-modified composite material was 10.6% higher than that of the cementitious material. The direct tensile bond strength of the polymer-modified composite material with various waterborne epoxy resin content significantly improved, demonstrating a maximum increase of 72.6%. Compared with the original cementitious material, the toughness, tensile deformation capacity, and tensile strength of the polymer-modified superfine cementitious composite material were improved. The maximum tensile amount increased by 48.3% when an appropriate amount of waterborne epoxy resin was mixed, which is the primary performance in long-term waterproofing. Moreover, the bearing capacity increased by 335.2% compared with the cementitious materials when 7% waterborne epoxy resin was mixed. The key contribution of this research is to propose a high performance and effective polymer-modified composite material for the treatment of waterproofing and plugging. The findings from the study also provide industry practitioners with a comprehensive guide regarding the mechanical and impermeability performances of the polymer-modified superfine cementitious composite material.