A computed scanning technology was applied to measure fracture tomography, and three-dimensional fracture meshes were established. Water flow experiments and simulations on fractures were conducted. Results demonstrate both Forchheimer and Izbash equations can capture the nonlinear flow behavior. As Reynolds number increases, contact obstacles and roughness of fracture increase the complexity of the velocity distribution by generating eddies or back flow. Nonlinear coefficient in Forchheimer equation increases by 1–5 orders of magnitude, ranging from 6 × 1010 to 5 × 1015. A critical Reynolds number is proposed to quantify the onset of nonlinear flow. Further quantitative analysis is conducted regarding flow path tortuosity.