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Nanofluids have become important working fluids for many engineering applications as they have better thermal properties than traditional liquids. Thus, this paper addresses heat transfer rates and entropy generation for a Fe3O4/MWCNT-water hybrid nanoliquid inside a three-dimensional triangular porous cavity with a rotating cylinder. The studied cavity is heated by a hot wavy wall at the bottom and subjected to a magnetic field. This problem is solved numerically using the Galerkin finite element method (GFEM). The influential parameters considered are the rotating cylinder speed, Hartmann number (Ha), Darcy number (Da), and undulation number of the wavy wall. The results showed that higher Da and lower Ha values improved the heat transfer rates in the cavity, which was demonstrated by a higher Nusselt number and flow fluidity. The entropy generation due to heat losses was also minimized for the enhanced heat transfer rates. The decrease in Ha from 100 and 0 improved the heat transfer by about 8%, whereas a high rotational speed and high Da values yield optimal results. For example, for Ω = 1000 rad/s and Da = 10−2, the enhancement in the average Nusselt number is about 38% and the drop in the Bejan number is 65% compared to the case of Ω = 0 rad/s and Da = 10−5. Based on the applied conditions, it is recommended to have a high Da, low Ha, one undulation for the wavy wall, and high rotational speed for the cylinder in the flow direction.