Starting from the issues related to the construction and management of customs supervision places for railway and water transportation, this paper systematically analyzes the problems and challenges in the facility layout of customs operation places, the construction of a public platform for customs and port logistics monitoring, the utilization of information and data, and the intensity of technological innovation. Based on in-depth research, this paper attempts to propose improvement strategies and suggestions in terms of scientifically planning the layout of customs supervision places for railway and water transportation, improving the operation of the logistics monitoring public platform, developing and utilizing the information and data system, building a smart customs, and innovating the supervision mode. This aims to further optimize the customs supervision process, improve supervision efficiency and accuracy, and provide a reference for the facilitation and safe development of international trade.