Aeromagnetic compensation plays a vital role in geomagnetic navigation and has received considerable attention throughout last few decades. Classical aeromagnetic compensation methods based on the Tolles–Lawson (T-L) model are mainly aimed at permanent, induced, and eddy-current magnetic interferences of aircraft platform, which ignores other stray magnetic field interference on the platform including the interferences caused by on-board electronic (OBE) systems. In order to cooperate with TL model, magnetometers are usually required to be installed on the extension rod outside the cabin, which is widely applied to geophysical magnetic survey. In order to ensure safety and reduce the cost of platform modification in geomagnetic navigation, it’s necessary to place magnetometers inside the cabin. It also further exacerbates the magnetic interferences and improves the difficulty of magnetic compensation. In this paper, a modified aeromagnetic compensation method is proposed, and the in-cabin OBE interferences are respectively modelled to be proportional to the currents and their temporal variations of different electronic devices. To ensure that modified model adapts to strong OBE interference in the cabin, a cut-off frequency determination method based on curvature calculation and a feature selection method based on correlation calculation are proposed. The cut-off frequency determination method helps to select passband filter which suitable for in-cabin OBE interference. The feature selection method can help to effectively select current and voltage inputs for modified model. In addition, principal component analysis (PCA) is adopted to reduce multicollinearity which is intensified by the extension of OBE interferences in coefficient-estimating. Experiments on public dataset are conducted to illustrate the effectiveness of the proposed method, and the best compensation result achieved 1.71nT of root mean square error (RMSE).