The numerical solution of the stable basic flow on a 3-D boundary layer is obtained by using local ejection, local suction, and combination of local ejection and suction to simulate the local rough wall. The evolution of 3-D disturbance T-S wave is studied in the spatial processes, and the effects of form and distribution structure of local roughness on the growth rate of the 3-D disturbance wave and the flow stability are discussed. Numerical results show that the growth of the disturbance wave and the form of vortices are accelerated by the 3-D local roughness. The modification of basic flow owing to the evolvement of the finite amplitude disturbance wave and the existence of spanwise velocity induced by the 3-D local roughness affects the stability of boundary layer. Propagation direction and phase of the disturbance wave shift obviously for the 3-D local roughness of the wall. The flow stability characteristics change if the form of the 2-D local roughness varies.