Abstract: To address the issues of unreasonable calculation of traditional ecological base flow, and the difficulty in adapting to practical application demands, this paper took the main control sections of the Baohe River and Xushui River, the primary tributaries of the Hanjiang River, as an example. The Mann-Kendall (MK) test was used to detect mutation points in the runoff sequence, and divided the sequence into subsequences. The ecological base flow of each subsequence was calculated using 14 hydrological methods. The comprehensive ecological base flow was obtained by taking the weighted average of these subsequence ecological base flows. By screening the results, the variable interval of ecological base flow was obtained. Finally, the mid-long term and short term guarantee degrees of ecological base flow were analyzed. The results showed that: (1) The variable interval of ecological base flow could better be adapted to complex and changing environments, which was more reasonable and feasible to implement. (2) For the Hedongdian section, the upper and lower limits of the ecological base flow were 3.02 to 34.64 m3/s and 0.78 to 13.71 m3/s, respectively. For the Shengxiancun section, the upper and lower limits of the ecological base flow were 2.21 to 31.28 m3/s and 0.57 to 12.51 m3/s, respectively. (3) The guarantee degrees for the Hedongdian section were higher than those for the Shengxiancun section. The guarantee degrees for the lower limits of the ecological base flow exceeded those for the upper limits. The mid-long term guarantee degrees of the ecological base flow were higher than those for the short term. The guarantee degrees in dry years were significantly lower than those in wet and normal years. These results provided a scientific basis for the rational development and utilization of water resources, as well as for the construction of ecological civilization of the Baohe River and Xushui River.