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This paper presents a dynamic model estimation using system identification (SI) technique and a multivariable controller design for an unmanned surface vehicle (USV) with two fixed thrusters. The catamaran shaped USV has been developed for marine research and surveying exploration in costal area. To validate the automatic control performance of USV, which is designed by classical PID controller, we carried out experiments to keep the USV's position at a fixed point and to track predefined positions. As a result, we have found that it needs time-consuming efforts to tuning the weight between heading and speed controller since the yawing and surge motions are tightly coupled to the two thrusters. In order to solve the problem, it is necessary to introduce the multivariable controller design method. And a numerical dynamic model is required for the model based design. This paper addresses the estimation of a dynamic model of the USV based on the experimental results and the design of Linear-Quadratic (LQ) controller based on a multivariable control method. To verify the efficiency of the designed controller using the estimated dynamic model, numerical simulations were carried out.