Based on the automatic dynamic analysis of mechanical systems (ADAMS), a virtual prototype of a multi-body collaborative operation system for the twin-ship joint lifting in specific scenarios is constructed to predict and evaluate the roll stability of the blocks to be removed during the new integrated dismantling operation of twin-ship joint lifting. The topological model of the system is constructed, and geometric parameters are used to describe the rolling motion characteristics of the topside in the system. Through the virtual prototype simulation, the most dangerous instability state of topside under different coupling motions of two vessels is explored, and the influence law of the ratio of vertical distance and horizontal distance from the center of gravity of topside to the connection point on the rolling angle is given. The results show that the test data-driven virtual prototype technology can effectively evaluate the motion characteristics of the topside in the complex multi-body system, which is consistent with the theoretical formula of the rolling instability angle of the topside obtained from the geometric topology model. The coupling motion of the two vessels at the same phase rolling and anti-phase heave has the greatest influence on the rolling stability of the topside. The ultimate aspect ratio of the topside obtained by the virtual prototype simulation can be used as the rolling stability evaluation parameters of the multi-body system, and provide a reference for the selection of engineering schemes.