A deep-tow magnetic survey was conducted in the northeastern margin of the Japan Basin during the GH96 cruise aboard the R/V Hakurei-maru in 1996, using a new deep-tow observation system with multiple sensors. Surface magnetic and seismic reflection data were also taken simultaneously. A deep-tow magnetic anomaly (amplitude: 775 nT; wavelength: 8 km) was detected, while no obvious anomaly was observed at the surface. In order to explain both surface and deep-tow magnetic features, we applied a two-dimensional forward modeling taking the results of ODP deep-sea drilling at Site 795 and the surface seismic reflection data in consideration. We obtained a magnetized layer with its top at the depth of acoustic basement, which well reproduced both of the observed magnetic anomalies. Comparison of the magnetic model with the seismic reflection data indicates that there is a good correlation between magnetization high and strongly reflecting basement. The correlation may be associated with the age and structure of the volcanic basement rocks. Magnetic data at different altitude levels, thus, showed that they can give better constraints on the depth of the source layer.