Three-dimensional intelligent engineering management and control systems (EMCS) based on the browser/server (B/S) model are an important part of intelligent engineering development. These systems are used for solving the difficulties encountered in engineering management with frequent cross-specialties and are vital tools for data exchange and service sharing among multiple departments. Currently, most engineering management and control systems are based on service-oriented architectures (SOAs). The integration mechanism and high coupling of SOAs leads to the reduction in system expansibility, service quality and service safety of the engineering system, making it difficult for these architectures to serve the construction of long-span valve hall engineering. To address these concerns, the management and application technology of the multidisciplinary data of valve hall engineering based on a microservice architecture (MSA) is proposed to improve the management efficiency of engineering data. A 3D integration modeling method for valve hall engineering structures and geological environments is proposed to establish the topological association between engineering structures and geological environments, without increasing the amount of model data required. A 3D intelligent engineering management and control technology for the entire process of the construction of long-span valve hall engineering is proposed, which realizes the entire process simulation and control of engineering construction based on WebGL technology. Accordingly, a three-dimensional intelligent engineering management and control system for the entire construction process of a long-span valve hall project in Southeast China is established, which can effectively manage and apply the data, display and analyze the three-dimensional model, and control and make decisions regarding the construction schedule. This study provides support for the construction of "smart engineering", promotes information communication and transmission between different project units, and speeds up the transformation from traditional construction management relying on drawings to three-dimensional intelligent construction management based on cloud services.