In the process of navigation, ships are inevitably affected by various disturbances on the sea level. Dynamic positioning(DP) refers to a technology that ships can still maintain a certain position or navigate along a fixed track under the existence of external disturbances. Compared with the traditional anchor positioning method, DP technology has the advantages of strong mobility, deep-sea operation and high positioning accuracy. The anti-disturbance control problem of dynamic positioning system of ships with slowly varying environmental disturbances and complex nonlinear term is investigated in this paper. Firstly, the fuzzy logic system is used to approximate the complex nonlinear term in the dynamic positioning system of ships. Secondly, to estimate the slowly varying environmental disturbances with partially-known information, an adaptive disturbance observer(ADO) is constructed. Based on this, an elegant anti-disturbance control(EADC) strategy is proposed by integrating disturbance observer based control(DOBC) and fuzzy control algorithm to achieve high accuracy anti-disturbance control. Finally, the simulation results on supply ship model are presented to demonstrate the effectiveness of the proposed strategy.