Industrial Ecology involves the transformation of industrial processes from linear to closed loop systems: matter and energy flows which were initially considered as wastes become now resources for existing or new processes. In this paper, Thermoeconomics, commonly used for the optimization and diagnosis of energy systems, is proposed as a tool for the characterization of Industrial Ecology. Thermoeconomics is based on the exergy analysis (Thermodynamics) but goes further by introducing the concepts of purpose and cost (Economics). It is presented in this study as a systematic and general approach for the analysis of waste flow integration. The formulation is based on extending the thermoeconomic process of the cost formation of wastes in order to consider their use as input for other processes. Consequently, it can be applied to important Industrial Ecology issues such as identification of integration possibilities and efficiency improvement, quantification of benefits obtained by integration, or determination of fair prices based on physical roots. The capability of the methodology is demonstrated by means of a case study based on the integration of a power plant, a cement kiln and a gas-fired boiler.