In order to establish a unified spatial reference for the whole ship, inertial matching measurement of hull deformation is widely used because of its continuity and concealment. However, the vibration-shock signal of shipborne equipment often brings short-time output disturbance to the user-side fibre gyroscope unit (FGU), and the disturbance will bring great challenges to the accuracy and convergence of inertial matching measurement. To solve these problems, the authors put forward a new algorithm named as attitude quaternion matching method-improved double factor adaptive Kalman filter-parameter adaptive Kalman filter (AQM-IDFAKF-PAKF). (1) The AQM established the FGU attitude as observation to build the basic model for hull deformation inertial matching method. (2) The authors introduced IDFAKF to track the trend of dynamic hull deformation in vibration interference by using historical data. (3) After judging the anti-vibration-shock calculation stop node, PAKF was utilised to adaptively adjust the parameters of hull deformation matching after vibration-shock, so as to quickly calculate the static hull deformation angle after shock interference. Numerical simulation results illustrated that the AQM-IDFAKF-PAKF can quickly converge the calculation of hull deformation angle with a small steady-state error under the condition of vibration-shock signal interference.