Abstract: The magnetic interference issue encountered by the magnetometer on a Mars explorer was investigated. A comprehensive magnetic control scheme was developed and implemented. An extended bracket, utilizing the solar array deployment structure, was designed to position the magnetometer far from the explorer body. Magnetic moment allocation indicators were established for each subsystem and major magnetic interference source component. The magnetometer sensor layout was optimized to minimize interference. Hysteresis and eddy current effects were rigorously controlled, and reasonable wiring techniques were employed. Consequently, the magnetism of the explorer’s major components was significantly reduced. Test results demonstrate that the interference impact is within 1 nT, thereby meeting the stringent accuracy requirements for the Mars explorer’s magnetic field measurements. This magnetic control approach provides a valuable reference for the magnetic design and control of other interplanetary spacecraft.