Asymmetries in boundary condition are inevitable in practice in microfluidic channels, despite being rarely addressed from theoretical perspectives. Here, by arriving at closed form analytical solutions, we bring out a unique coupling between asymmetries in surface charge and heat transfer in electroosmotically driven microchannel flows. For illustration, we assume that the channel is laterally composed of two parts, each having specified values of the zeta potential and the wall heat flux. Considering low zeta potentials, we obtain analytical solutions in terms of infinite series for the dimensionless forms of the electric potential, the velocity, and the temperature distributions. We demonstrate that, by carefully adjusting the governing parameters, a variety of flow patterns may be achieved, a property that is crucial in applications such as liquid-phase transportation and mixing. Moreover, we show that the average velocity is a linear function of both the zeta potential ratio and the coverage factor. We further show that the average Nusselt number increases when part of the channel having the larger heat flux enlarges and the zeta potential of the part having the smaller surface charge increases. Hence, the maximum heat transfer rates are achieved when the boundary conditions are symmetrical.