A UAV remote sensing load storage device was designed by taking a certain type of UAV as the flight platform. Considering the problems of magnetometer errors and carrier magnetic interference in measurement, we proposed a method for magnetic field measurement error compensation based on Particle Swarm Optimization (PSO). The data measured by the triaxial magnetometer was taken as the system input, and PSO was used to solve the magnetic interference compensation model. After the magnetic field data of the target signal was obtained, it was compared with the geomagnetic field data obtained from the optical pump magnetometer, which was taken as the real scalar value. The experimental results showed that the PSO based error compensation method in magnetic field measurement has higher compensation precision and certain value for engineering application.