Implementing electrophysiological recordings within an MRI environment is challenging due to complex interactions between recording probes and MRI-generated fields, which can affect both safety and data quality. This study aims to develop and evaluate a hybrid electromagnetic (EM) simulation framework for efficient and accurate assessment of such interactions. Methods: A hybrid EM strategy integrating the Huygens’ Box (HB) method with sub-gridding was implemented in an FDTD solver (Sim4Life). RF coil models for mouse and rat head were simulated with and without intracortical (IC) and epicortical (EC) graphene-based micro-transistor arrays. Three-dimensional multi-layered probe models were reconstructed from two-dimensional layouts, and transmit field (B₁⁺), electric field (E), and specific absorption rate (SAR) distributions were evaluated. Performance was benchmarked against conventional full-wave multi-port (MP) simulations using Bland-Altman analysis and voxel-wise percentage differences. Results: HB simulations reduced computational time by approximately 70-80%, while preserving spatial patterns of |B₁⁺|, |E|, and SAR, including transmit-field symmetry and localized high-field regions. Deviations from MP were minimal for |B₁⁺| (median Δ % 0.02-0.07% in mice, -3.7% to -1.7% in rats) and modest for |E| and SAR, with absolute SAR values remaining well below human safety limits. Graphene-based arrays produced negligible effects on RF transmission and SAR deposition. Conclusion: The HB approach enables computationally efficient, high-resolution evaluation of EM interactions involving microscopic probes in MRI environments, supporting simulations that are otherwise impractical with full-wave MP modeling.