Exploring the development of an indicator system for multidimensional comprehensive observation is of great significance for the integrated management of wetland resources, theoretical research, and related decision making. Starting from the integrated management of resources, this study expounded the characteristics and significance of three-dimensional comprehensive observation of wetland resources and analyzed the current status of wetland resources observation in China. It combined the uniqueness and complexity of wetland resources and characteristics of three-dimensional comprehensive observation, proposed the principles of development of the indicator system, and constructed an atmospheric-surface-underground indicator system of multidimensional comprehensive observation of wetland resources, which is consisted of 5 first-level indicators of climate resources, biological resources, surface water resources, soil resources, and groundwater resources, 18 second-level indicators, and 31 third-level indicators. The system aims to provide long-term, continuous, and stable observations of wetland resources in order to realize the transformation of wetland resource management from empirical to data-driven decision making, from extensive to scientific and precision development and utilization, and from the protection of single resource elements to the protection of all resources of mountains, waters, forests, croplands, and grasslands.