The material’s wettability plays an important role in the field of micro-fluid flow. In this paper, the effect of material’s wettiability on heat transer performance of fluid flowing through the microchannel has been investigated by numerical approach. The process of the hot liquid flowing through a microchannel with cold walls, whose materials possess different wettabilities, is simulated by lattice Boltzmann method (LBM). The results indicate the heat transfer performance is deteriorated with surface hydrophobic property becomes better. It is because that, for thehydrophobic material, the attractive force of the fluid/solid interaction is small and the flow velocity will be larger which will lead to heat exchang become insufficient. Especially, for the ideal-hydrophobic material, the heat transfer coefficient will be reduced notably. In this case, a gas formed between liquid and soild surface will play a role of the heat insulating layer since the thermal conductivity of the gas is relatively small compared to that of liquid.