Industrial ecosystem is an artificial system established in industries under the guidance of the theory of industrial ecology. Similar to a natural ecosystem, an industrial ecosystem achieves circulation of materials and utilization of energy cascade through cooperation between the enterprises and the organizations within a certain range of time and space. Construction of a successful industrial ecosystem can use waste to replace raw materials, utilize energy extracted from nature, reduce raw material and energy consumption, and curtail waste management costs, resulting in economic and environmental benefits. Research on industrial ecosystems, both locally and internationally, has gained importance and has become vital for promoting sustainable development of the society. At the same time, research on industrial ecosystem has been promoted in many areas and fields. Results from these studies provide significant scientific guidance to our society in achieving social and economic development while making optimal use of resources, reducing environmental pressures, transforming the traditional industries into more advanced ones, and upgrading the industrial eco-efficient level. It is increasingly accepted that construction of an industrial ecosystem is the key to realizing a circular economy, and it is a practical and important tool for achieving sustainable development. However, there are a number of practical problems in developing an industrial ecosystem. To address these, there is an urgent need to strengthen the research inputs for industrial ecosystem, especially, in order to discover, enhance, and improve their structure and efficiency, and thus promote its sustainable development. At present, qualitative studies on industrial ecosystems are relatively more, and include studies on their concept, characteristics, construction principles, and business philosophy. Quantitative studies about the system mechanism are few, and many of these are conducted using the Index Evaluation System. This approach, especially for integration research on systems,has drawbacks. The essence of the management of industrial ecosystem is to regard and manage the economic activities and the natural environment as an organic whole, and to establish a new mode of management that integrates the ecological and the economic dimensions. Given these, this paper discusses four innovative quantitative methods to study industrial ecosystem from a systems perspective. These include emergy analysis, exergy method, ecological footprint, and ecological information analysis. The theoretical basis, development process, application, and characteristics of these methods are summarized in detail. Finally, based on the basic principles of the theory of industrial ecology (which are, 1. integration of ecological and economic dimensions, 2. the long term resilience of system, and 3. considering the extensive and intensive properties at the same time), we conducted a comprehensive comparison of these methods with an intent to provide direction and reference for future research on industrial ecosystems.