High-fidelity models capable of accurately predicting ship motion are critical for promoting innovation and efficiency in the maritime industry. However, creating an advanced model that comprehensively represents the system and its interaction with dynamic environments has always been challenging. Many models provide partial knowledge about a system. To handle the deficiency and improve model fidelity, in this artile, we propose a hybrid modeling methodology, in which prior knowledge describing the ship dynamic effects is incorporated into a data-driven calibrator, yielding a representative model with high predictive capability. Enabled by the integration of model estimated ship states into the calibrator, the informative information could be interpreted and carried forward. Simulation and full-scale experiments are conducted on the research vessel Gunnerus to exemplify the concept. A best available numerical model and a neural network are prepared to be the foundation and calibrator, respectively. Experiment results show that the cooperative model greatly improves the predictive capability of the research vessel. From the ship modeling perspective, this study provides new insights by bridging the gap between two separate domains: 1) model-based and 2) data-driven.