The water-lubricated stern tube bearing carried on the extreme working like heavy-duty, low-velocity and starting operation condition, the interface of water-lubricated bearing always suffers from the severe abrasive wear. Carbon nanofibers have been widely used as additives to enhance the properties of composites used in water-lubricated bearings. Therefore, it is important to determine and characterize the wear-resistant mechanisms of composites reinforced with carbon nanofibers. In this work, molecular dynamics (MD) simulation is employed to investigate the mechanical and tribological properties of ultra-high molecular weight polyethylene (UHMWPE) composites and determine the interactions and wear mechanisms of the UHMWPE composites from the atomic level perspective. Three-layer models (Cu-Composites-Cu) were developed to simulate the deformation and wear process of the composites. The effect of three different directions of the carbon nanotubes (CNTs) on the mechanical and tribological properties of the composites was calculated and analyzed. The results demonstrated that, compared to that of the pure UHMWPE, after CNT reinforcement, the shear modulus of the three CNTs/UHMWPE composites increased by 28.04%, 42.22%, and 47.4%, respectively, while the wear rate decreased by 16.91%, 41.05%, and 47.37%, respectively. When the CNTs are perpendicular to both the sliding direction and the top Cu layer can significantly reinforce the matrix materials and provide better mechanical and tribological properties. This study provides a theoretic basis for the structural design and performance enhancement of water-lubricated bearings.