In this paper, a perturbation method is introduced to study the EOF in a microparallel channel with 3D wall roughness. The corrugations of the two walls are periodic sinusoidal waves of small amplitude in two directions either in phase or half-period out of phase. Based on linearized Poisson-Boltzmann equation, Laplace equation, and the Navier-Stokes equations, the perturbation solutions of velocity, electrical potential, and volume flow rate are obtained. By using numerical computation, the influences of the wall corrugations on the mean velocity are analyzed. The variations of electrical potential, velocity profile, mean velocity, and their dependences on the wave number and of wall corrugations in two directions, the nondimensional electrokinetic width K, and the zeta potential ratio between the lower wall and the upper wall sigma are analyzed graphically.