The study of the thermal contact resistance at the liquid–solid interface is an important subject of the heat transfer of phase change materials. In this work, a fractal model for predicting the thermal contact resistance at the liquid–solid interface is established by considering the self-affine fractal geometry of the rough surface. Based on the fractal characteristic of roughness structures, topographical and mechanical analyses have been conducted to identify the position of the liquid–solid interface and determine the thermal contact resistance at the interface. The relationship between contact parameters and the thermal contact resistance are studied. Based on the analytical predictive model for thermal contact resistance at the liquid–solid interface, the three-dimensional melting process of a nanoparticle-enhanced phase change material with different thermal contact resistances was simulated by using the finite volume method, and the enthalpy-porosity model is employed. The effects of thermal contact resistance between the composite phase change material and the heat source are investigated. It is found that the augmentation of thermal contact resistance decreases the melting and heat transfer rates and the influence of thermal contact resistance becomes more pronounced with a higher volume fraction of nanoparticles.