In the present study, MHD mixed convection inside an electromagnetic pump, with Cu-water nanofluid as the working fluid, has been analyzed numerically. To find the best heat transfer and pumping performance, an in-house parallel lattice Boltzmann code is developed to solve the problem in a 3D domain. The nanofluid flows in pump's channel by Lorentz force caused by permanent magnetic and DC electric fields which are acting perpendicular to each other. By considering a hot element with constant temperature in contact with the side wall, natural convection forms perpendicular to the forced flow. The study has been conducted for the certain pertinent parameters of Rayleigh number, magnetic field strength, electric field strength and the nanoparticle volume fraction. Results are investigated in terms of fluid flow, heat transfer and entropy generation. Numerical results indicate that due to the fluid flow, heat transfer performance has an optimum point in Ha = 200 where increasing S and Ra numbers only shows positive effects on Nu. For low Rayleigh numbers where the forced convection is dominant, increasing nanoparticles has minor impact on Nusselt. So, in this case addition of nanoparticles to the base fluid is not beneficial. Also, entropy generation decreases by increasing Rayleigh number and nanoparticles’ volume fraction or decreasing S.