Abstract Numerical investigation was conducted for fluid flow and heat transfer in microchannel cooling passages. Effects of viscosity and thermal conductivity variations on characteristics of fluid flow and heat transfer were taken into account in theoretical modeling. Two-dimensional simulation was performed for low Reynolds number flow of liquid water in a 100 μm single channel subjected to localized heat flux boundary conditions. The velocity field was highly coupled with temperature distribution and distorted through the variations of viscosity and thermal conductivity. The induced cross-flow velocity had a marked contribution to the convection. The heat transfer enhancement due to viscosity-variation was pronounced, though the axial conduction introduced by thermal-conductivity-variation was insignificant unless for the cases with very low Reynolds numbers.