Autonomous underwater vehicles (AUVs) are advanced near-bottom platforms that can be used for magnetometric analysis of the seafloor. However, the vehicle itself can cause interference with the magnetic measurements, which need to be corrected. Here, we derive a functional relation between the magnetic measurements and AUV's heading that is based on the composition and causes of an AUV's near-bottom magnetic anomaly. We set up a method to correct tri-axial magnetometer interference caused by the AUV. Magnetic induction intensity is removed using magnetic data collected during the spinning of the AUV. Connatural magnetic field of the AUV is collected and subtracted by using portable magnetometer. The method performs very well during QianlongII AUV experimental tests performed on land and in lake. The method also corrects magnetic data by an autonomous benthic explorer (ABE) AUV and yields good results. The effects of main components of QianlongII AUV on the magnetic measurement results are analyzed and make sure dominating interference produced by the batteries. That is mitigated using a probe extension pole. Furthermore, excellent survey data and satisfactory correction results are obtained during the AUV sea trials. This verifies the efficacy of the proposed method for correcting tri-axial magnetometer interference caused by AUV.