Abstract: In view of the riparian area of main stream Heilongjiang River that is influenced by the embankment construction, a watershed ecosystem health assessment system is constructed based on the pressure state response (PSR) model. And a watershed ecosystem health assessment model is applied to the ecological health assessment of the administrative regions along the river, which is based on analytic hierarchy process and fuzzy matter element theory. The results show that the ecological health values of Mohe County, Heihe City, Tongjiang City and Fuyuan County were 0.6793, 0.7283, 0.7314 and 0.7558 before disturbance while the values were 0.6023, 0.5805, 0.6117 and 0.7026 after disturbance; for Mohe County and Fuyuan County, the ecological health level maintained "sub-health" and "health" while Heihe City and Tongjiang City degraded to "sub healthy"; the corresponding ecological damage degree of the four areas were 11.34%, 20.29%, 16.37% and 4.39%. In addition, according to the evaluation index system, the ecological health problems in the 4 cities are analyzed comprehensively and some countermeasures are put forward.