Take Qiangwei river in Yancheng city as the research object, based on factor analysis and optimized nonlinear grey Bernoulli model, combined with the water quality data from 2009 to 2017, the paper analysizes the water quality improvement and the governance effect of the main pollution factor of comprehensive treatment of black and smelly water. Results show that the implementation of comprehensive treatment of black and smelly water makes Qiangwei river water quality improved obviously, the life pollution and nutrient pollution control effect is obvious. But inorganic pollution and water physical environment improvement effect is not obvious, so further formulation and implementation of corresponding measures is needed.The results also provide reference and basis to plan the objectives and tasks in next phase of comprehensive treatment of black and smelly water.