Estimation and compensation for hull deformation is an indispensable step for the ship to establish a unified space attitude. The existing hull deformation measurement methods are dependent on the pre-established deformation model, and an inaccurate deformation model will reduce the deformation estimation accuracy. To solve this problem, a hull deformation estimation method without deformation model is proposed in this article, which utilizes the neural network to fit the hull deformation. To train the neural network online, connection weights of the neural network are regarded as system state variables which can be estimated by the Unscented Kalman Filter. Simultaneously, considering the time delay problem of inertial data, a time delay compensation method based on the quaternion attitude matrix is proposed. The simulation results show that the proposed method can obtain high estimation accuracy without any deformation model even when the inertial data are asynchronous.