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A novel analysis of the electromagnetohydrodynamic (EMHD) non-Newtonian nanofluid blood flow incorporating CuO and Al2O3 nanoparticles through a permeable walled diseased artery having irregular stenosis and an aneurysm is analyzed in this paper. The non-Newtonian behavior of blood flow is addressed by the Casson fluid model. The effective viscosity and thermal conductivity of nanofluids are calculated using the Koo-Kleinstreuer-Li model, which takes into account the Brownian motion of nanoparticles. The mild stenosis approximation is employed to reduce the bi-directional flow of blood to uni-directional. The blood flow is influenced by an electric field along with a magnetic field perpendicular to the blood flow. The governing mathematical equations are solved using Crank-Nicolson finite difference approach. The model has been developed and validated by comparing the current results to previously published benchmarks that are peculiar to this study. The results are utilized to investigate the impact of physical factors on momentum diffusion and heat transfer. The Nusselt number escalates with increasing CuO nanoparticle diameter and diminishing the diameter of Al2O3 nanoparticles. The relative % variation in Nusselt number enhances with Magnetic number, whereas a declining trend is obtained for the electric field parameter. The present study’s findings may be helpful in the diagnosis of hemodynamic abnormalities and the fields of nano-hemodynamics, nano-pharmacology, drug delivery, tissue regeneration, wound healing, and blood purification systems.