In the conventional hull deformation measurement method, the external measurement noise is considered constant. However, due to the complex sea conditions and the high-frequency chatter caused by the waves, the measurement noise is colored noise. The aim of this paper is to develop a hull deformation measurement method based on fiber optic gyro (FOG) angular rate matching in complex sea conditions. On the one hand, the traditional system model is optimized to reduce the dimension, and a simplified linear state space model is proposed. On the other hand, a finite impulse response (FIR) low-pass digital filter is designed and introduced into the angular rate matching measurement method, so that the deformation estimation accuracy can still be maintained in complex sea conditions. The simulation and swing table test are designed to verify the effectiveness of the hull deformation measurement method proposed in this paper. The results show that the proposed method in this paper can effectively eliminate external noise interference and improve estimation accuracy.