Aeromagnetic exploration is a magnetic exploration method that detects changes of the earth’s magnetic field by loading a magnetometer on an aircraft. With the miniaturization of magnetometers and the development of unmanned aerial vehicles (UAV) technology, UAV aeromagnetic surveying plays an increasingly important role in mineral exploration and other fields due to its advantages of low cost and safety. However, in the process of aeromagnetic measurement data, due to the ferromagnetic material of the aircraft itself and the change of flight direction and attitude, magnetic field interference will occur and affect the measurement of the geomagnetic field by the magnetometer. The work of aeromagnetic compensation is to compensate for this part of the magnetic interference and improve the magnetic measurement accuracy of the magnetometer. This paper focused on the problems of UAV aeromagnetic survey data processing and improved the accuracy of UAV based aeromagnetic data measurement. Based on the Tolles–Lawson model, a numerical simulation experiment of magnetic interference of UAV-based aeromagnetic data was carried out, and a radial basis function (RBF) artificial neural network (ANN) algorithm was proposed for the first time to compensate the aeromagnetic data. Compared with classical backpropagation (BP) ANN, the test results of the synthetic data and real measured magnetic data showed that the RBF-ANN has higher compensation accuracy and stronger generalization ability.