With a development history of less than 20 years, it is time for industrial ecology to define its academic scope and theoretical basis. This paper first reviews the four main areas of industrial ecology: (1) Social metabolism, the well-developed area of industrial ecology. It provides macro-level methods and tools to observe and measure the linkages between economic development and material flows. The further research is to refine and strengthen the material flow picture and mechanism behind it; (2) Industrial symbiosis, the main characteristics of the industrial ecology fields. It is in fact the re-understanding of industrial system from waste exchanging perspectives. A unified framework with stringent rules of logic will benefit the development of industrial symbiosis theory and practice; (3) Infrastructure, cities and regional economic systems, a series of objects with spatial characteristics. Infrastructure and industries, with mutual co-evolution relationship, together constitute the material basis for the city, and then the city is the subset of the regional economic system. This group of fields needs to deal with conflicts resulting from the globalizing nature of the industry and the localization nature of social and ecological factors; (4) the diversity, complexity and sustainability of industrial development, the theoretical core of industrial ecology. All these bring great challenges to research agenda of industrial ecology, and remind us to avoid falling into the trap of simplistic reduction. Finally, four important directions are presented, following the definition of the academic scope of industrial ecology from ontology, methodology and metaphor guidelines.