Resource and environmental elements as controlling factors for ecologic and socio-economic are crucial to seek new ideas and paths for development and prosperity. In this study, environmentally-extended input-output analysis and ecological network analysis were combined to develop three ecological networks including energy ecological network, water ecological network, and carbon ecological network for searching the complex relationships among different departments for water utilization, energy consumption, and carbon emissions under considering China as a superorganism with various complex metabolic processes and the most fundamental metabolic materials. The embodied ecological elements intensity, the indirect consumption and emissions, the embodied material flows, the ecological relationships, and the dependence intensities among sectors was obtained through transforming the monetary input-output data to physical data from 2007, 2012, and 2017. The results show that the Energy Ecological Network and Water Ecological Network were in a relatively stable state with a mutualism index greater than 1, and the relationship among different sectors in the CO Ecological Network needs to be further adjusted. AM (Advanced Manufacture) and Agr (Agriculture) played the top exporter and importer roles with AM as the largest embodied energy consumer and CO emitter, and Agr as the largest embodied water user. More measures about resource conservation and emission reduction for AM and Agr are desired. Con (construction) had a strong dependence intensity on other sectors with amounts of over 90%. Resources and environmental effects on Con can be improved by increasing the utilization efficiency of intermediate products. The results could provide scientific policy implications and guidelines to promote the stable and healthy operations by revealing the dynamic change of sectors within the Energy-Water-CO metabolic system in China.