Identification of parameters involved in the linear response model with high precision is a highly cost-effective, as well as a challenging task, in developing a suitable model for the verification and validation (V+V) of some key techniques for autonomous vessels in the virtual testbed, e.g., guidance, navigation, and control (GNC). In order to deal with this identification problem, a novel identification framework is proposed in this paper by introducing the extended state observer (ESO), and the well-evaluated robust weighted least square support vector regression algorithm (RW-LSSVR). A second-order linear response model is investigated in this study due to its wide use in controller designs. Considering the highly possible situation that only limited states could be measured directly, the required but immeasurable states in identifying parameters contained in the response model are approximately estimated by the ESO. Theoretical analysis of the stability is given to show and improve the applicability of the ESO. Simulation studies based on linear response models with predefined parameter values of a cargo vessel and a patrol vessel maneuvering in an open water area are carried out, respectively. Results show that the proposed approach not only estimates immeasurable states with high accuracy but also ensures good performance on the parameter identification of the response model with very close values to the nominal ones. The proven identified approach is economic because it only requires limited kinds of low-cost sensors.@en