In this article electrokinetic mixing through heterogeneous microchannels has been studied and the effects of slip coefficient, zeta-potential, Debye-Hückel parameter and Reynolds number on mixing efficiency have been investigated. The microchannels studied here, have non-homogenous zeta-potential distribution at the wall, while other surface properties are considered to be homogenous. In order to investigate the electro-osmotic mixing, the Navier-Stokes, Nernst-Planck, Laplace and convection-diffusion equations have been solved numerically for velocity field, ions distribution, electrical potential and concentration field, respectively. The entropy of concentration distribution has been used as a quantitative index to evaluate the mixing performance. The results show that the behavior of electro-osmotic micromixers strongly depends on the amount and distribution of wall zeta-potential and in most cases the mixing efficiency increases with reduction of slip coefficient or Debye-Hückel or Reynolds number. It is found that in presence of slip, mixing efficiency decreases at low Reynolds numbers, while increases at high Reynolds numbers. Also, the accuracy of Helmholtz-Smoluchowski approximate model is investigated and it is found that the performance of the Helmholtz-Smoluchowski model in predicting the mixing efficiencies deteriorates for high wall zeta-potential or low values of Debye-Hückel parameter.