In this research, a self-made three-axis magnetic field sensor device is designed and installed on a drone, which will be able to measure a large area of environmental magnetic fields. The designed magnetic field sensor adopts the air-coil sensing principle, and is equipped with a 3D printed sensor structure to ensure the orthogonality of the three-axis sensing directions. In addition, the drone will generate electromagnetic field, which will affect the measurement data of the designed three-axis magnetic field sensor. Therefore, a two-stage signal processing mechanism is designed to extract the sensing signal (fundamental and harmonic components) that only belongs to the environmental magnetic field. Finally, the measured magnetic fields are transmitted back to the remote monitoring system via ZigBee wirelessly. Since an aerial camera is installed in the drone, and the operator can remotely control the drone to measure the magnetic field of a large-scale path.