The invention relates to a fluxgate aeromagnetic data processing method based on machine learning, and the method comprises the following steps: obtaining data preprocessing, determining training data, building a machine learning model, training the machine learning model based on the training data, and predicting three-component fluxgate aeromagnetic data based on the trained machine learning model. The method has the advantages that the technical advantages of machine learning and the accuracy of optical pump data are utilized, a model can be established and trained, fluxgate data can be predicted, so that steering errors are reduced, the data quality is improved, and the aeromagnetic exploration effect is achieved, and the method is particularly suitable for fluxgate unmanned aerial vehicle aeromagnetic exploration and three-component aeromagnetic exploration application.