Global environmental concerns require a constant reduction in carbon emission from the shipping industry, and it has become an irreversible trend to replace traditional fossil energy with advanced energy storage technology. The application of large-scale lithium battery in all-electric ships is still in its infancy, and rare research has been conducted on the state of charge (SOC) estimation and energy management optimization for all-electric ships. In this paper, an optimal energy efficiency management strategy of all-electric vessels based on precise SOC estimation is proposed to maximize the propulsion load while ensuring service loads. Furthermore, a model-based Unscented Kalman Filter is utilized to estimate SOC of the onboard lithium battery. With the help of the proposed method, the operation cost is reduced, and the arrival time is shortened.