The characteristics of electrokinetic flow in a microchannel depend on both the nature of surface potentials, that is, whether it is uniform or nonuniform, and the electrical potential distribution along the channel. In this paper, the nonlinear Poisson-Boltzmann equation is used to model the electrical double layer and the lattice Boltzmann model coupled with the constraint of current continuity is used to simulate the microfluidic flow field in a rectangular microchannel with a step variation of surface potentials. This current continuity, including surface conduction, convection, and bulk conduction currents, has often been neglected in the literature for electroosmotic flow with nonuniform (heterogeneous) microchannels. Results show that step variation of ion distribution caused by step variation surface potential will influence significantly the electrical potential distribution along the channel and volumetric flow rate. For the system considered, we showed that the volumetric flow rate could have been overestimated by as much as 70% without consideration of the current continuity constraint.