In order to achieve the sustainable management and efficient use of natural resources, long-term, stable, and continuous comprehensive observations are necessary for acquiring basic resource data and information on resource types, quantity, quality, and processes of interactions. It is necessary to construct an indicator system of the comprehensive observation of natural resources. However, due to the lack of a unified indicator system of natural resources observation in China, there exist big gaps in observation and management between different regions, which make it difficult to standardize the management and improve the utilization of natural resources on a national scale. Hence, a scientific, systematic, and normative indicator system of comprehensive observations, which can be applied on a national scale in China, is urgently needed. Based on the primary issues to be addressed and with reference to the existing indicator systems in China and internationally, the authors summarized the basic principles of establishing the indicator system and the selection of indicators. On the basis of the classification of natural resource elements, the authors established a comprehensive observation indicator system that consists of 36 classification modules, 6 comprehensive observation subsystems, and several functional modules, by a combination of forward and inverse inference methods, modularization, and other construction methods. Through the establishment of a multidimensional comprehensive observation network across the atmosphere-surface-subsurface levels and the individual-landscape-regional scales, the data of natural resource elements can be obtained and the management, evaluation, and utilization of natural resources can be achieved.