Based on the five criteria of hydrological integrity, chemical integrity, morphological structure integrity, biological integrity and social service function, the river health assessment index system for the Gansu section of the Weihe River Basin was constructed. The combined weighting method based on the improved analytic hierarchy process and the Critic method, and the fuzzy matter-element extension model were used to calculate the assessment grade of the river health. The river health in the Gansu section of the Weihe River Basin was evaluated and the prominent problems of water health of the Weihe River were analyzed with the obstacle diagnosis model. The results show that from 2017 to 2019, the health levels of the main stream of the Gansu section of the Weihe River Basin were in a sub-health state but with a slight improvement trend. The chemical integrity of the five criteria layers was the worst, indicating that the watershed management should pay more attention to the river water quality management. The indicators for assessing the sensitivity of river sections are related to the hydrological, chemical and biological integrity, and are the most effective sensitive factors to improve the river health level.