The objective of the numerical study is to explore the effects of transverse magnetic field on heat transfer and fluid flow characteristics in a trapezoidal microchannel heat sink. The effects of the channel bottom width, channel top width, channel height and Hartmann number on heat transfer and fluid flow characteristics are widely investigated. In addition, effects of nanoparticles type (Al2O3, SiO2, CuO, ZnO), base fluid type (water and ethylene glycol) and its concentration (0–4%) under the influence of magnetic field are also investigated. The governing equations for three-dimensional steady, laminar flow and conjugate heat transfer of a microchannel are solved using the finite volume method. The acquired results are discussed in detail. The results reveal that the magnetic field can increase the thermal performance.