In the context of harsh emission control and ecological environment protection, the shipping industry is transforming and upgrading towards greening, decarburization, and electrification. Battery-powered all-electric inland ships have been attracting increasingly attention. However, its initial investment cost is much more expensive than a traditional diesel-driven mechanical ship because lithium-ion batteries are currently expensive. Hence, a suitable battery size and efficient energy management strategy for ship sailing are very important for a battery-powered ship. In this paper, a novel joint optimization method of the sailing speed and battery capacity, which considers the interaction between battery size and sailing speed as well as multiple operation factors, such as freight demand and battery life, and port electricity price, is proposed to fully exploit the battery-powered ships’ application potential. Moreover, a joint optimization model of the sailing speed and battery energy consumption model considers the battery-powered ship’s characteristics and waterway characteristics. Next, a solution algorithm for the proposed joint optimization model is established to achieve joint decision-making regarding the sailing speed and battery size. Finally, case studies are conducted to demonstrate the flexibility and effectiveness of the proposed method. The results show that the proposed method can obtain the optimal sailing speed and the corresponding battery capacity synchronously when the actual transportation scenario is fixed. Moreover, the battery initial investment cost can be effectively reduced with the prosed method.