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A superconducting quantum interference device (SQUID) planar gradiometer is an extremely sensitive sensor for magnetic gradient measurements. It has been shown to have potential applications for aeromagnetic detection. The major challenge when operating an aeromagnetic SQUID system in actual environment is the motion noise, including the inherent response resulting from gradiometer imbalance and from magnetic interferences. Three orthogonal reference magnetometers are usually adopted to improve the gradiometer balance. However, magnetic interference coming from the system itself also needs to be compensated. In this article, a mathematical model of the motion noise picked up by the gradiometer is derived from the traditional magnetic total field compensation method. Based on the model, the signals from the triaxial magnetometer can also be used to compensate the eddy current contribution to the magnetic interference. To verify the compensation method, a SQUID planar gradiometer system was set up and used for flight trials. The gradient field noise and imbalance of our homemade gradiometer were measured to be 100 fT/m/rt(Hz) and 2E-4 in the lab. In flight, the motion-induced peak-to-peak output of the gradiometer was reduced from 170 to about 0.1 nT/m, so that a magnetic anomaly signal of about 2 nT/m from a cargo ship was clearly recognized. [ABSTRACT FROM AUTHOR]