Abstract City interaction, though of great importance in the context of market-oriented economy, has rarely been studied quantitatively compared to structure and function inside the city due to the tribulation when acquiring and disposing the relational data between cities. Herein, we quantified city-to-city relations in ecological and economic contexts with the application of emergy analysis, which proved to be a promising approach to evaluating various city flows on a common basis. Emergy diagram of urban system was constructed, and the related relational data were chosen from the ecological and economic aspects respectively to form two integrated indicator systems incorporating the transfer of labor, material and currency, etc. Based on the ecological and economic emergy of urban system, the city-to-city sustainability index was established to identify the sustainable conditions of the two cities, and hopefully, it could reveal potential complementarity or competition between these cities over time. With the introduction of emergy analysis, this study provided a new way to quantify city interaction; it might also shed light on how an enhancement and amelioration of inter-city cooperation could substantially contribute to the sustainable development on a regional scale.