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Aeromagnetic survey of multi-rotor UAV is widely used in small and medium-sized mineral resources survey, engineering investigation, non-explosive detection and other fields due to its advantages of high safety, low cost and convenient operation. The original data of UAV aeromagnetic survey includes interference from external environment, interference from UAV platform and interference from airborne electromagnetic equipment. The interference is mainly shown as striping anomaly along the direction of the survey line in the aeromagnetic anomaly map, which affects the accuracy of aeromagnetic compensation and information detection of geological anomaly body, thus affecting the accuracy of interpretation of geological anomaly body. In this paper, the algorithm of Variational Modal Decomposition (VMD) is introduced to filter and preprocess the aeromagnetic data to obtain high quality aeromagnetic data. At the same time, the source and characteristics of the errors are predicted according to the interference size and spectrum characteristics of the Modal function errors, which provides a reference for the optimization of aeromagnetic system.