By combing the basic characteristics of river system in Fujian Province and summarizing the selection principle of ecological flow control section, four categories and 44 ecological flow control sections with different control objectives were selected. Based on the requirement and working conditions of river ecological protection, the control objectives of ecological flow in each section are determined by hydrological analysis. The distribution density of control section is tested, and the rationality of ecological flow control target is tested according to water resources allocation pattern and project dispatching ability. The results show that section setting and ecological flow control goal are reasonable and effective, which can meet the requirement of national ecological civilization experimental area in Fujian Province.