The paper is devoted to construction the special the software complex for analysis, synthesis and modeling of the control system for marine vessels. The complex is designed in MATLAB-Simulink package. It contains mathematical and computer model of the controlled object, mathematical and computer model of controller and tools for visualization. This software complex is universal for all objects with similar mathematical model and it can be easily modified for any marine vessel. In the paper the structure of software complex is given. Its work is illustrated by an example of real vessel #CSOC1120.