Industrial symbiosis is an option to reduce waste and to improve resource productivity by exchanging usable wastes or byproducts between neighboring industries. While case examples of industrial symbiosis have mainly been conducted in industrial areas, the application of industrial symbiosis to rural areas should be carefully examined as a means to revitalize local agriculture, forestry, and related industries. A method for planning a system with industrial symbiosis is strongly needed in order to extract the essence of systems integration among different industrial process systems. In this study, a systematic procedure for planning industrial symbiosis in rural areas is proposed. Firstly, the planning problems to be solved for application of industrial symbiosis were characterized by comparing the conditions in industrial and rural areas based on activity modeling applied in systematic chemical process design. The procedure for planning industrial symbiosis to solve specified problems was visualized as an activity model. Focusing on the simulation of changes in material and energy flows within characterized planning problems, the data structure activating the specified activities was constructed by data modeling. The developed activity and data models were validated through the demonstration of actual case examples of industrial symbiosis in rural areas. The clarification of similarities and differences among various areas and industries based on such modeling facilitates the planning of industrial symbiosis.