Matrix nanocomposites are superior-performing substances with distinct features and design possibilities. Due to their exceptional thermophysical characteristics, they can be utilized in various applications ranging from packaging to biological uses. This groundbreaking work focuses on magnetized hybrid nanofluids disperse polymeric/ceramic matrix nanocomposites substances while flowing between orthogonal porous coaxial disks. The study also investigates the significance of the permeability value ( \(\:{A}_{*}\) ) they are concerning the permeability Reynolds number and the extending/shrinking ratio. The impact of nanoparticles on flow and thermal transmission properties is examined, and the mathematical framework and empirical relationships for nanocomposite substances are expressed as partial differential equations before being converted into ordinary differential equations using relevant variables. The precise numerical solution is obtained using Runge-Kutta and shooting techniques. Important engineering physical variables are utilized to calculate variations in skin friction coefficient, Nusselt value, and Sherwood rate readings at the top and bottom walls of the discs. The study presents an effective nanolayer thermal conductivity and non-effective nanolayer thermal conductivity contrast table and graph. The results demonstrate that increasing the thickness of the nanolayers from 0.4 to 1.6 improves effective nanolayer thermal conductivity and heat transfer, and increasing the volume percentage of hybrid NPs from 2% to 6% enhances Nusselt value. Moreover, under shrinking flow conditions ( \(\:{\alpha\:}_{*}\:>0\) ), the hybrid nanofluid (PTFE–SWCNT/H₂O) shows a thermal enhancement of 9.37–9.67% in Nusselt number compared to the single nanofluid (SWCNT/H₂O), highlighting the role of morphology-tuned nanolayers in boosting thermal transport. This innovative work could be beneficial for nanotechnology and related nano-sized components.