The lid-driven top wall’s influence combined with the side walls’ waviness map induce the mixed convection heat transfer, flow behavior, and entropy generation of a hybrid nanofluid (Fe3O4–MWCNT/water), a process analyzed through the present study. The working fluid occupies a permeable cubic chamber and is subjected to a magnetic field. The governing equations are solved by employing the GFEM method. The results show that the magnetic force significantly affects the working fluid’s thermal and flow behavior, where the magnetic force’s perpendicular direction remarkably improves the thermal distribution at Re = 500. Also, increasing Ha and decreasing Re drops both the irreversibility and the heat transfer rate. In addition, the highest undulation number on the wavy-sided walls gives the best heat transfer rate and the highest irreversibility.