The Yinma River Basin in Jilin Province was taken as a case to study the ecological operation in this paper. The basin ecological operation model was established and a two-period calculation software system was also developed. Moreover, the ecological operation results and ecological operation line of reservoirs were given for maintaining water supply condition of existing reservoirs and supporting irrigation districts, and ecological operation cost was analyzed in detail. The research results can provide scientific and technological support for scientific management and reasonable scheduling of water conservancy projects in the Yinma River Basin.