The irregular morphology of single rock fracture significantly influences subsurface fluid flow and gives rise to a complex and unsteady flow state that typically cannot be appropriately described using simple laws. Yet the fluid flow in rough fractures of underground rock is poorly understood. Here we present a numerical method and experimental measurements to probe the effect of fracture roughness on the properties of fluid flow in fractured rock. We develop a series of fracture models with various degrees of roughness characterized by fractal dimensions that are based on the Weierstrass-Mandelbrot fractal function. The Lattice Boltzmann Method (LBM), a discrete numerical algorithm, is employed for characterizing the complex unsteady non-Darcy flow through the single rough fractures and validated by experimental observations under the same conditions. Comparison indicates that the LBM effectively characterizes the unsteady non-Darcy flow in single rough fractures. Our LBM model predicts experimental measurements of unsteady fluid flow through single rough fractures with great satisfactory, but significant deviation is obtained from the conventional cubic law, showing the superiority of LBM models of single rough fractures.