Combined effects of thermal radiation and variable viscosity on a time-dependent boundary-layer flow of magnetic nanofluids over a rotating disk in the presence of the porous medium have been numerically investigated. To carry out the study, hydrocarbon based magnetic nanofluid containing magnetite Fe3O4 particles of 10 nm with magnetic phase concentration of 10% has been taken. For numerical solutions of the modelled system containing the governing equation of the flow, a MATLAB tool ODE45 is employed with shooting technique for the initial guess of the unknown boundary conditions. The flow phenomenon and heat transfer on the plate surface are characterised by various flow parameters such as viscosity variations, unsteady rotation parameter, Prandtl number, and radiation parameter. Also, a comparative thermal analysis has been carried out for magnetic nanofluids having three different bases viz. hydrocarbon, fluorocarbon, and water. Results reveal that heat transfer rate of hydrocarbon base magnetic nanofluids is 73.4511% faster than water base magnetic nanofluids, and 239.7458% faster than fluorocarbon base magnetic nanofluids. This enhanced heat transfer capacity of hydrocarbon base magnetic nanofluids will help in improving the performance of oil and ore extraction drilling systems used in mining industry and other geothermal applications.