This paper develops a set of ships draft detection system in pitch-up setting, adopting the method of distance measurement with ultrasonic sensor array to achieve the ships 3D draft dynamic testing. The system is installed on the pontoon; therefore, the swinging of the pontoon will affect the stability of the detection system due to the wind and waves and water flow situation, and the deflection change of structure frame under water will also affect the measurement accuracy of the system. In order to solve the above problems, the system uses dynamic pressure compensation algorithm to compensate the system data in real time. The random noise in the data can be processed by median filtering algorithm. The least square method is used to fit the depth of the ship's draught, the influence of ship stern's noise is eliminated, and the depth of the ship's draught is finally obtained. The algorithm has been verified by experimental data, and the results show that this algorithm is fast and effective. The on-site ship test shows that the accuracy of the system meets the requirements.