In this study, active mixing in a microchannel with spatiotemporal variations in zeta potential distributions was investigated theoretically. In this mixing system, the primary flow is a pressure-driven flow (i.e., parabolic flow), and the electro-osmotic recirculating rolls induced by the heterogeneous zeta potential distributions act as the perturbation source. By timewise alterations of two different electro-osmotic recirculating flow fields, chaotic mixing can be induced. Blob deformation, Poincaré map, and Lyapunov exponent analyses were employed to describe the behaviors of the particle motion in this active mixing system. Finally, the optimal time-switching period was identified, which was also verified through direct numerical simulations.