In 1994, Sino-Japan cooperative cruise for shipboard three-component magnetic field test was carried out in northern region of the South China Sea, using new Shipboard Three Component Magnetometer (STCM) developed by the Earthquake Institute of Tokyo University. About 2 500 km (6 lines) field survey data were acquired successfully. According to the magnetic boundary strike diagram (MBSD) method proposed by Seama N et al., the author analyzes these data and points out that the MBSD method can be used to express types of magnetic boundary synthetically and visibly. The author then conducts comparative analysis on the calculated result and the verified magnetic lineation of northern South China Sea basin and finds that they agree with each other very well. That study suggests that the MBSD method is useful when dealing with STCM data and studying marine magnetic structure.