The present paper investigates the steady laminar flow and thermal mixing performance of non-Newtonian Al₂O₃ nanofluids within a two-layer cross-channel micromixer, employing three-dimensional numerical simulations to solve the governing equations across a low Reynolds number range (0.1 to 50). It also addresses secondary flows and thermal mixing performance with two distinct inlet temperatures for thin nanofluids. Additionally, it explores how fluid properties and varying concentrations of Al₂O₃ nanoparticles impact thermal mixing efficiency and entropy generation. Simulations were conducted to optimize performance by adjusting the power law index (n) across different nanoparticle concentrations (1–5%). The findings show that magnetohydrodynamics can enhance mixing efficiency by generating vortices and altering flow behavior, providing important guidance for improving microfluidic system designs in practical applications.