We conducted deep-sea magnetic measurements using autonomous underwater vehicles in the Bayonnaise knoll caldera, the Izu-Ogasawara island arc, which hosts the large Hakurei hydrothermal field. We improved the conventional correction method applied for removing the effect of vehicle magnetization, thus greatly enhancing the precision of the resulting vector anomalies. The magnetization distribution obtained from the vector anomaly data shows a ∼2 km wide belt of high magnetization, trending NNW-SSE going through the caldera, and a low-magnetization zone ∼300 m by ∼500 m in area, extending over the Hakurei site. Comparison between the results obtained using the vector anomaly and the total intensity anomaly shows that the magnetic field is determined more accurately, especially in areas of sparse data distribution, when the vector anomaly rather than the total intensity anomaly is used. We suggest a geologically motivated model that basaltic volcanism associated with the back-arc rifting occurred after the formation of the caldera, resulting in the formation of the high-magnetization belt underneath the silicic caldera. The Hakurei hydrothermal field lies in the intersection of the basaltic volcanism belt and the caldera wall fault, suggesting a mechanism that hot water generated by the heat of the volcanic activity has been spouting out through the caldera wall fault. The deposit apparently extends beyond the low-magnetization zone, climbing up the caldera wall. This may indicate that hot water rising from the deep through the alteration zone is transported laterally when it comes near the seafloor along fissures and fractures in the caldera wall.