Conjugate heat transfer in a microchannel with a slip boundary condition imposed on the channel's walls by a uniform magnetic field is studied. The working fluid consists of a Water/Ag mixture nanofluid. A preconditioned lattice Boltzmann method (LBM), formed by combining the incompressible LBM with the regular LBM, is applied to the velocity field and temperature field, respectively. The microchannel's upper wall is thermally isolated when a constant heat flux is imposed on the basin of the microchannel. The simulations are carried out under a variety of different conditions, e.g., various Reynold numbers, Re = 50 and 150, nanoparticle concentrations (φ = 0, 3%), slip coefficients (0 ≤ B ≤ 0.03), and Hartmann numbers (0 ≤ Ha ≤ 30). Surface hydrophobicity results in a reduction of surface friction of up to 46% at B = 0.03 and Ha = 30. The surface friction reductions at Ha = 0, 10, and 20 are 15%, 27%, and 38%, respectively. These results indicate that as the surface slip increases, the drag resisting the fluid dynamics decreases. Moreover, adding the nanoparticles to the base flow can improve the heat transfer by 50%. Besides, using the magnetic field increase the shear stress and, consequently, the drag force dramatically (up 340%). On the other hand, the magnetic field enhances the heat transfer by improving the fluid velocity near the wall, while its effect on the Nu number improvement is not more than 20%. As a result, the magnetic power should be controlled to achieve the best heat transfer performance with the lowest pumping energy consumption.