Magnetic nanoparticle hyperthermia has emerged as a promising method in cancer treatment. However, the aggregation behavior of Fe3O4 nanoparticles under intense magnetic fields remains poorly understood. This study mathematically models the flow of a Casson fluid embedded with both aggregated and non-aggregated Fe3O4 nanoparticles to assess their effect on heat transfer efficiency. Porosity ( \(\beta _{1}\) ), magnetic field (M), Prandtl number (Pr), heat generation parameter ( \(Q_0\) ), and nanoparticle volume fraction ( \(\phi \) ) are analyzed, considering velocity and temperature profiles, skin friction ( \(C_\textrm{fr}\) ), and Nusselt number (Nu). The coupled nonlinear partial differential equations are nondimensionalized and solved using the bivariate spectral weighted residual method, and validation is confirmed through the finite element method. The results show that with aggregation, \(C_\textrm{fr}\) decreases by 16.13% as \(\phi \) rises from 0.05 to 0.06, compared to 0.73% without aggregation. As \(Q_0\) increases, \(C_\textrm{fr}\) rises by approximately 0.13% with aggregation, compared to 0.15% without aggregation. Furthermore, as \(\phi \) increases with aggregation, Nu decreases by 16.14% compared to 0.73% without aggregation. The higher \(\beta _{1}\) and stronger M decrease velocity. The temperature profile increases with \(\phi \) for both aggregated and non-aggregated nanoparticles, indicating enhanced energy dissipation. These results demonstrate the potential of \({\text{F}}{{\text{e}}_3}{{\text{O}}_4}\) nanofluids to improve hyperthermia in cancer treatment.