In this study, laboratory experiments and simulations have been conducted to investigate single water phase flow through self-affine rough fractures. It is the first time that 3D printing technology is proposed for the application of generating self-affine rough fractures. The experimental setup was designed to measure the water volume by dividing the discharging surface into five sections with equal distances under constant injection flow rates. Water flow through self-affine rough fractures was simulated numerically by using the Lattice Boltzmann method (LBM). An agreement between the experimental data and the numerical simulation results was achieved. The fractal dimension is positively correlated to fracture surface roughness and the fracture inclination represents the gravity force acting on the water flow. The influences of fracture inclinations, fractal dimensions, and mismatch wavelengths were studied and analyzed, with an emphasis on flow paths through a self-affine rough fracture. Different values of fractal dimensions, fracture inclinations, and mismatch wavelengths result in small changes of flow rates from five sections of discharging surface. However, the section of discharging surface with the largest flow rate remains constant. In addition, it is found that the gravity force can affect flow paths. Combined with the experimental data, the simulation results are used to explain the preferential flow paths through fracture rough surfaces from a new perspective. The results may enhance our understanding of fluid flow through fractures and provide a solid background for further research in the areas of energy exploration and production.