The autopilot system of vessel is proposed to take service safety and security, to elevate service efficiency, to decrease labor and to improve working environment. Ultimate purpose of the proposed system is to minimize the number of crew by guaranteeing economical efficiency of shipping service. Recently, the research is being achieved to compensate various nonlinear parameters of vessel and apply it to course keeping control, track keeping control, roll-rudder stabilization, dynamic ship positioning and automatic mooring control etc. using optimizing control technique. Relation between rudder angle controlled by steering machine of vessel and ship-heading angle, and load condition of ship is nonlinear, which affects various parameters of shipping service. The speed and direction of waves, velocity and quantity of wind, which also cause the non-linearity of it. Therefore the autopilot system of ship requires the robust control algorithm can overcome various non-linearity. On this paper, we design the autopilot system of ship, which overcomes nonlinear Parameters and disturbance of it using Fuzzy Algorithm, evaluate the proposed algorithm and its excellence through simulation.