Electromagnetic positioning technologies are frequently-used in surgical navigation systems to achieve precise position of surgical instruments in bodies. Still, in operating rooms with complex environments, they would be disturbed by eddy currents of metals. This paper explores a calibration method to mitigate eddy current interference. Initially, The study examined the generation mechanisms of eddy currents and established the expression of secondary magnetic fields they produced, which exhibited a 90-degree phase difference with the AC excitation field. Subsequently, an integral calibration method was proposed, leveraging fields’ distinct phases for separating. Through simulation, various metal materials were modeled to study their impact on magnetic fields. The effectiveness of the calibration method was evaluated by comparing positioning accuracy before and after calibration. Results demonstrated over 80 % average calibration efficiency, effectively mitigating errors induced by metals and enhancing the system’s reliability. This calibration method is crucial for the broader application of electromagnetic positioning systems.