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The investigation of thermal radiation and thermophoretic impacts on nano-based liquid circulation in a microchannel has a significant impact on the cooling of microscale equipment, microliquid devices, and many more. These miniature systems can benefit from the improved heat transfer efficiency made possible by the use of nanofluids, which are designed to consist of colloidal dispersion of nanoparticles in a carrier liquid. Understanding and precisely modeling the thermophoretic deposition (TPD) of nanoparticles on the channel surfaces is of utmost importance since it can greatly affect the heat transmission properties. This work examines the complex interaction between quadratic thermal radiation, magnetohydrodynamics, and TPD in a permeable microchannel. It aims to solve a significant knowledge gap in microfluidics and thermal and mass transport. The governing equations are simplified by applying suitable similarity restrictions, and computing solutions to the resulting equations is done using the Runge‒Kutta Fehlberg fourth‒fifth-order scheme. The results are shown using graphs, and significant engineering metrics are analyzed. The outcomes show that increased Eckert number, magnetic, and porous factors will improve the thermal distribution. Quadratic thermal radiation shows the greater thermal distribution in the presence of these parameters, while Linear thermal radiation shows the least thermal distribution. The rate of thermal distribution is higher in the linear thermal distribution case and least in the nonlinear thermal radiation case in the presence of radiation and solid fraction factors. The outcomes of the present research are helpful in improving the thermal performance in microscale devices, electronic devices cooling, health care equipment, and other microfluidic applications.