With the increasingly strict regulations for the energy-saving and emission-reduction technology of ships, minimizing fuel cost and thus reducing the carbon intensity index (CII) is one of the most critical issues in the design and operation of merchant ships. More recently, many wind-assisted devices, such as rotors, wind sails, etc., have been investigated and designed to utilize renewable wind energy. With the equipment of wind-assisted rotors, the optimization of ship routes becomes more important because the effect of this wind-assisted device highly depends on the local wind field along the shipping route. In this paper, an improved ship weather routing framework based on the A* algorithm has been proposed to determine the optimal ship route and ship operations with wind-assisted rotors. The proposed framework effectively utilizes different sources of data, including ship design, weather forecasting and historical sailing information, to produce a better estimation of fuel consumption under the effect of sea states. Several improvements on the classic A* algorithm, including directed searching and three-dimensional extension, are proposed to improve the routing effect and efficiency. Finally, the proposed method was applied to test cases of a VLCC operating from China to the Middle East and the results show that the total fuel consumption could be reduced compared to the minimum distance route.