To solve the influences of time delay between Inertial Measurement Unit(IMU) data on measuring accuracy in the attitude matching measurement of ship deformation, a time delay estimation method was established. Firstly, the ship deformation data measured by optical devices were proposed to confirm a mathematic model of ship deformation process. Then the local attitude information from high-accuracy master-Inertial Navigation Sytem(INS) and slaver-INS was used to match the inertia and Kalman filter equations were used to estimate the ship deformation. Moreover, the time delay parameters were added into the Kalman filter to estimate and compensate the time delay. Finally, an IMU data synchronous read device was designed to verify the effectiveness of proposed algorithm. Experimental results show that compensation results by IMU data synchronous read device and the algorithmic are similar to optical measurement data, and the pitch errors, rolling errors and the heading errors are 13″, 12″ and 5″, respectively. These results demonstrate that the Kalman filter estimates the time delay effectively, compensates the time delay and improves the measurement accuracy of ship deformation.