Ship deformation is one of the physical phenomena that restrict the mission effectiveness of ship weapon systems. Aimed at how to measure the deformation of ship accurately， a method based on joint matching of angular increment and attitude matrix for measuring ship deformation is proposed. This method only relies on gyroscopes which can provide angular motion information of carrier， trough reliable strategy to estimation ship deformation， under the condition that initial alignment and the velocity-position update for inertial navigation are not required， high precision measurement for ship deformation can be achieved. Simulation experiments show that estimation accuracy of the proposed method has is better than 35″(Root mean square)， which can provide support for scenes that requires ship deformation information such as alignment， artillery launch.， etc.