In recent years, with the development of shipping industry, the mass of greenhouse gases (GHG) emissions originating from ships is also increasing rapidly. To reduce the GHG emissions from ships, designing the optimised routes with higher energy use efficiency is becoming more important for ships navigating in short seas. Based on the innovative application of energy efficiency operational index (EEOI), a route optimisation model is established. To solve the model, we divide one single voyage into several voyage segments and consider the variable speed across voyage segments. Then the navigation strategy is used to find out the sailing route of the minimum EEOI value, this sailing route is called as the green route. Finally, numerical experimental results show that the EEOI values of the experimental groups which used the optimised navigation method are 4.67%-16.95% lower than that of the control group. The results demonstrate that the green route designed in this paper can effectively improve the energy use efficiency of ships.@en