Under the impact of climate change and human activities, hydrological sequence has undergone some changes and its consistency broken. Many existing hydrologic methods for environmental flow analysis are facing a great challenge by this. This paper presents a combined approach of mutation point identification, hydrologic frequency method, and hydraulic method of ecological water depth and velocity, focusing on solution of the problems of broken consistency and zero flow in hydrological sequence. In this approach, first the locations of extracted mutation points were obtained and different stages of hydrological variation were delimited according to these locations and the interference degree of human activities. Then, the hydrologic data in the stages that were taken separatedly as a natural sequence, near natural sequence, and human-disturbance hydrological sequence, were used to determine their minimum flows and suitable flow ranges for river ecological health. Finally, the environmental flows at the dam-site of the Wenyu river reservoir under natural conditions were obtained with the hydrology frequency method and hydraulic method. And based on these runoffs, ecological guarantee rates were calculated for different stages. The results provide a developing trend of the eco-hydrological system of the Wenyu river.