As an innovative means to promote low-carbon and ecological development of cities, sponge cities have attracted extensive attention from industry and scholars. Measuring the operation efficiency of a sponge city can effectively measure whether the current input and output are reasonable, whether the management and operation are scientific, etc., which can find out the weaknesses in the current process and management. This paper proposes an evaluation method of interval cross-efficiency combined with TOPSIS and DEA to measure the operating efficiency of a sponge city. Specifically, an evaluation system, that includes three inputs and six outputs, is established at first from the perspective of input and output. Secondly, due to the uncertainty of the natural environment, two DEA models of benevolent and aggressive models are adopted to obtain the cross-efficiency interval value of a sponge city. Next, the cross-efficiency interval values are aggregated based on TOPSIS, and then, the descending principle is introduced to rank sponge cities to obtain the optimal operation efficiency cities. Finally, a case is used to verify the effectiveness of the proposed method. The research idea of this paper is clear, the research method is simple, and the research results can provide a basis for building an efficient and high-level sponge city.