<p>This study presents a comprehensive analysis of the Cattaneo–Christov heat flux, Joule heating, and viscous dissipation effects on MHD hybrid nanofluid flow between orthogonal rotating permeable coaxial disks. Addressing a critical research gap, we investigate the thermal behavior of hybrid nanoparticles composed of metallic oxide and metal (Al₂O₃-Cu) dispersed in a water (H₂O) base fluid within the fluid domain. Our focus is on visualizing heat and mass transmission in a hybrid nanofluid under these unique flow conditions. The governing PDEs are converted into the system of non-dimensional ODEs, which are then numerically solved by combining the shooting methodology with the fourth-order <i>R</i>-<i>K</i> method. The findings are presented through detailed tables and graphical representation, offering valuable insights into the physical behavior of hybrid nanofluid flow. Key findings include a significant increase in the Sherwood number with rising activation energy parameter values (ranging from 1 to 9). While the Nusselt number increases with the augmented values of the Eckert number (ranging from 1 to 5). A stronger magnetic field enhances fluid velocity toward the center of the top disk while suppressing it near the lower disk. Additionally, nanoparticle volume fraction (ranging from 1 to 13%) and thermal relaxation parameters (ranging from 0.1 to 0.5) significantly enhanced the Nusselt number and thermal phenomena. This study provides a novel contribution to the understanding of hybrid nanofluid thermal management, with potential implications for advanced industrial and environmental applications.</p>