Improving the sustainability of traditional resource-based cities in China has been a core issue and policy-priority for Chinese government to establish long-term ecological civilization, particularly for northeastern China which is recognized as a typical agglomeration area of resources cities. In this study, we establish a three-layer index system consisting of a comprehensive layer, systemic layer, and variable layer, and including 22 indicators which are grouped into economic, social and environmental subsystems. After that, the TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) method was applied to measure and rank the sustainability of the selected 15 typical resource-based cities in northeast China, and then a GIS (Geographical Information System) technique based on the software of SuperMap was applied to map the sustainability in terms of the spatial effects among these cities. The results reveal that a unilateral improvement of a subsystem did not mean an improvement or contribution to whole system. In detail, during the past 15 years from 2000 to 2015, the comprehensive sustainability of resource-based cities in Northeastern China shows a declining trend in the mass, and the sustainability of the economic subsystem shows increase; the sustainability of the social system remains stable, while the environmental subsystem shows decrease. These situations might result from policy interventions during the past 15 years, therefore, promoting the sustainability of resource-based cities needs a historical approach, which should focus on the coordinated development of its economic, social, and environmental subsystems.