Natural convection enhanced by magnetic fields and nanofluids has broad applications in thermal management systems. This study investigates magnetohydrodynamic (MHD) natural convection in a wavy trapezoidal cavity containing centrally located heated square obstacles, filled with various nanofluids Cu–H
2O, Fe
3O
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Natural convection enhanced by magnetic fields and nanofluids has broad applications in thermal management systems. This study investigates magnetohydrodynamic (MHD) natural convection in a wavy trapezoidal cavity containing centrally located heated square obstacles, filled with various nanofluids Cu–H
2O, Fe
3O
4–H
2O, and Al
2O
3–H
2O. A uniform magnetic field is applied horizontally, and the effects of key parameters such as Rayleigh number, Ra (10
3–10
6), Hartmann number, Ha (0–50), and nanoparticle volume fraction,
φ (0.00, 0.02, 0.04) are analyzed. The numerical simulations are performed using the finite element method, incorporating a wavy upper boundary and slanted sidewalls to model realistic enclosures. Results show that an increasing Rayleigh number enhances heat transfer, while a stronger magnetic field reduces convective flow. Among the nanofluids, Cu–H
2O demonstrates the highest Nusselt number and ecological coefficient of performance (ECOP), whereas Fe
3O
4–H
2O exhibits superior performance under stronger magnetic fields due to its magnetic nature. Entropy generation, S
T decreases with increasing Ra and
φ, indicating reduced thermodynamic irreversibility. These results provide insights into designing energy-efficient enclosures using nanofluids under magnetic control.
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