Abstract: The free-running model test is an effective way to evaluate ship performance. In this paper, a Manipulation and Control (MC) system is designed for a new concept shuttle vessel. The MC system in-cludes two parts: an ashore control system and an onboard control system, and the two parts exchange infor-mation through a Wireless Local Area Network (WLAN). The actuators of the shuttle vessel are equipped with sensors to obtain the feedback data, and certain sophisticated programmable elements are incorporated as the drivers of the actuators, where the lower and upper computer software are both written in the Python programming language. The MC system is then successfully applied to the free-running model test of the new concept shuttle vessel. Experimental results indicate that the MC system is efficient in terms of the de-velopment effort, easy to be operated, and has good scalability and portability. The maneuverability of the new concept shuttle vessel is well demonstrated through the free-running model test results. Finally, the free-running experiment results tested with the MC system is compared with the actual towing tank data, which shows high consistency.