Numerical study of heat transfer of nanofluids has been conducted to investigate forced convective cooling in rectangular microchannel. A micro-electro-mechanical system is modelled by building with two heating resistors embedded in a silicon substrate. Microchannel made from polydimethylsiloxane is planted in the substrate with a length of 17.5mm. Two cross section areas with high and width of 100mm x 100mm and 100mm x 1000mm are being used for the study. TiO₂/water nanofluid with different volume fractions are used as the coolant. Because of the not well-insulated micro-electro-mechanical system, heat generated by the heating resistors will be lost to the surrounding as well as carried away by the nanofluids through the microchannel. Temperature variations along the microchannel is calculated based on the concept of conjugate convective heat transfer. Force convective heat transfer is analyzed at low Reynolds number for different nanofluid concentrations. Numerical results are compared with experimental data available in the literature.