This study considers the formation control problem of heterogeneous ships with unknown time-varying disturbances, dynamic uncertainties, and unmeasurable speeds, a robust adaptive output feedback formation control scheme for the heterogeneous ships based on nonlinear extended state observer is developed. In order to solve the heterogeneous ships formation control problem with leader-following structure, transforming the formation control problem into a class of ship trajectory tracking problem by improving the design of the virtual ship. Firstly, a nonlinear extended state observer is designed for estimating ship speeds due to technical limitations and external disturbances. Then, combining the adaptive neural networks with disturbances adaptive law to deal with the unknown time-varying disturbances and dynamic uncertainties. Meanwhile, the second-order tracking differentiator is designed to calculate the derivative of the virtual control law, which has higher precision comparing to the first-order filter. Stability theory is proved that all the signal of closed-loop control system are uniformly ultimately bounded, and the tracking errors can converge into arbitrary small neighborhoods around zero. Finally, comparative simulations were performed to demonstrate the effectiveness of the proposed controller.