This article reviews conventional methods applied in current urban metabolism studies. Based on the limitations of these conventional methods, it highlights two urgent methodological needs for urban metabolism research: the need for using different spatial and temporal scales and the need for addressing issues of sustainable development. In order to meet these urgent needs, we propose a research framework based on 3D geovisualization. The article argues that GIS and visualization can play an important role in enhancing the transparency and comprehensibility of the results of urban metabolism studies. Furthermore, it is also an effective platform for investigating urban metabolism at various spatial and temporal scales. Specifically, introducing the various speeds of flows and incorporating the differences in the rhythm of these flows will be helpful. GIS and visualization can help to translate analysis results into urban policy suggestions.