Numerical study of the effect of temperature and heat transfer as well as surface heterogeneity effects on mixing and electroosmotic flow in microchannels with convergent/divergent and straight mixing chamber is carried out. The fluid properties and surface zeta potentials are assumed to be temperature dependent. Based on the Nernst–Planck Poisson model, the governing equations of this problem include the Laplace equation, Poisson equation, Navier–Stokes and the propagation equation as well as the energy equation, respectively for the distribution of external electric field, distribution of internal electric field due to the charge of ions, fluid motion, concentration field and temperature distribution, which are solved by the finite element method. Flow rate, the mixing efficiency and a new parameter called mixing capacity, which is achieved by multiplying flow rate by mixing efficiency, are obtained for convergent/divergent and straight microchannels in a constant external electric field distributed under different wall temperatures, and performance of the geometries in flow transfer and mixing development is investigated. For electroosmotic flow, heterogeneous microchannels create vortices which improve mixing. Different arrangements of heterogeneous pieces of the surface create different patterns of vortices, each of which has different effects in the various geometries on fluid flow and mixing. Also, the dependence of the molecular diffusion on temperature causes increasing the mixing of species with the temperature increment. The results show that divergent microchannels have the maximum flow rate and the minimum mixing efficiency, but this efficiency can be increased by increasing the wall temperature. Convergent microchannels also have high mixing efficiency due to low flow rates and sufficient time for mixing even at low and near ambient temperatures, although their mixing capacity is less than the divergent microchannels.