The special crane used by ship in this paper is a multi-joints and folding robot arm’s work system. Because it needs to work in a variety of sea conditions and being affected by waves and so on, the high demands of the trajectory control should be required. For this kind of complex control system, a system which is analyzed and simulated by the combination of ADAMS (Automatic Dynamic Analysis of Mechanical Systems) modeling based on a virtual prototype and MATLAB control is built and designed. The composition and implementation of the system are presented in the paper. The fuzzy cerebella model articulation controller (FCMAC) was used to tracking control and dynamic simulation research was done for this system. The results showed the superiority of this method which made kinematics and dynamics modeling analysis on ship-borne special crane based on the ADAMS. The simulation results of controller showed FCMAC had good tracking effect. The research method has intuitive, efficient and convenient features, provide better thought for similar studies of complex mechanical system.