Abstract: Measurement of magnetic fields is one of the important tasks in deep space exploration missions. From magnetic fields, it is possible to explore the planetary interiors, to study the evolution of the planets, and to understand space environment of the Solar system. The fluxgate magnetometer based on the Faraday's law is used to measure the magnetic field. Due to its high adaptability, maturity and low cost, it is the most widely used magnetometry instrument in the deep space missions. The principles of the measurement, and the methods of the ground and in-orbit calibrations of the instrument are briefly reviewed. The applications of the instrument in deep space exploration missions are also introduced. At present, China has already been able to develop high precision fluxgate magnetometer for space applications. It is expected that the fluxgate magnetometer will play important roles in future deep space exploration missions.