The Tianmen-Hanbei River Basin is afflicted by aggravating problems, such as water use contradiction between life, production and ecology, degradation of water ecology and restriction of socio-economic development. In order to solve these problems, this study constructed a coupled water-economic society-ecological environment model based on water system theory and system dynamics method, so as to examine the suitability of in-stream ecological flow thresholds at the system level. With the application of the scenario simulation method, nine scenarios were set up to simulate the water resources supply and demand, along with economic and social development in the study area under high, medium and low ecological flow thresholds from 2022 to 2035, based on the uncertainty of future natural water supply and control measures such as efficient water conservation and increased utilization of reclaimed water. The results showed that both efficient water conservation and increased utilization of reclaimed water are beneficial for alleviating conflicts between regional water users caused by the increase of ecological flow thresholds. From the perspective of coordinated development of water-economic society-ecological environment, it is recommended that the ecological flow thresholds for wet years (P=25%) in the study area should be set at 30%-50% of annual runoff, while 10%-30% for normal years (P=50%) and dry years (P=75%). In addition, increasing ecological flow thresholds should be accompanied by regulatory measures to improve water resources utilization. This study investigates the suitability of ecological flow thresholds for rivers based on the water-economic society-ecological environment co-evolutionary mechanism, which provides a theoretical basis for the optimization and scientific management of complex water resources systems.