Magnetic positioning systems, as a key technology in minimally invasive surgical navigation, are highly susceptible to intraoperative electromagnetic interference, particularly from the spatial magnetic fields generated by current-carrying wires near surgical instruments. To suppress such magnetic interference and enhance instrument tracking stability, this study systematically proposes a magnetic interference suppression strategy based on the spatial structure optimization of wires, supported by numerical simulations and experimental validation. Using COMSOL Multiphysics® software, we established finite element models of two typical wiring structures—parallel wires and twisted pairs—and conducted a comparative analysis of their spatial magnetic field distributions under identical excitation currents. To further validate the simulation results, we constructed a high-precision experimental platform and employed a tri-axial fluxgate sensor to measure the magnetic fields of the two wire models under controlled conditions; the experimental data showed strong agreement with the simulation results. This work provides an optimized method for mitigating magnetic interference in surgical navigation systems, significantly improving intraoperative instrument positioning accuracy.