Multibeam system is a rather new technique for generating huge digital terrain model quickly. If the primitive data does not perform quality control and the calibration process, inconsistency among the axes of transducer, motion sensor and gyrocompass may results in unreasonable underwater topography. The problem in the hydrographic surveying in the practice is not easy to seek for the suitable seabed or underwater feature for patch test at present. This research attempts to use fewer horizontal cross section of an underwater feature to compute roll, pitch and yaw deviation angle that differs from traditional vertical profile computing approach for patch test. And using different survey line combination and different underwater topography condition to achieve independent solution of angle deviation . We also design the new processing order for patch test. It hopes to utilize this concept to carry out patch test by the common underwater feature or recycling man-made object for resolving this problem in the future. The experimental results show that new calibration can get the same achievement as the traditional calibration by the CARIS HIPS software, and the calibration results applied in the cross check lines can pass through IHO special standard. It shows that the calibration results not only suit for calibration survey lines, but also good for rest of the area. It proves the proposed new patch test is feasible.