The rapid adoption of battery-powered vessels is hindered by limited endurance and high investment costs. While battery swapping offers a rapid energy solution, deploying numerous integrated charging-and-swapping stations is economically inefficient. The “centralized charging, decentralized battery swapping” strategy leverages the advantages of both charging and swapping, enhancing infrastructure efficiency while controlling costs. This study proposes an optimization model for the joint planning of centralized charging centers and decentralized battery swapping stations. The model simultaneously considers construction costs, battery transportation logistics, and battery purchasing costs to minimize both capital and operational expenditures. Results demonstrate that coordinated battery scheduling significantly reduces the total number of batteries required, limits infrastructure expansion, and lowers over-all system costs. Application to a major inland shipping route demonstrates that the proposed model can reduce total costs by 13.95% compared to a conventional system of integrated stations. These findings underscore the importance of integrated infrastructure planning and highlight the economic and operational advantages of optimizing the deployment of charging and swapping systems.