Abstract: The traditional analytic hierarchy process shows the problem of the possibility of cumbersome calculation and serious inconsistency. Aiming at that, we comprehensively consider the advantages of the optimal transfer matrix and the "three-scale method" to establish an improved analytic hierarchy process. A waterway ecological evaluation system, which consisted of 1 target, 6 criteria, and 17 indicators, was constructed with reference to the basis of existing research. Taking the Jingjiang Reach of the Yangtze River as an example, we evaluated and compared the situation of the waterway regulation works in 2011 (before regulation) and 2015 (after regulation) and concluded that the Channel Health Index (I_CH) increased from “good” (in 2011 with I_CH=3.432) to “excellent” (in 2015 with I_CH=4.187). The ecology of the Jingjiang Channel exhibited significant improvement after the waterway regulation works. The 6 functions under the criterion level are classified into 4 types of influencing factors, according to the reasons for the increase of the health index. The relative deviations of the results calculated by the improved analytic hierarchy process and the traditional analytic hierarchy process are 0.94% (2011) and 0.40% (2015), respectively, which means that the improved analytic hierarchy process simplifies the evaluation scale of the comparison matrix and optimizes the consistency of the matrix while ensuring the accuracy of the calculation results.