In order to evaluate the work of regional river chief system, 25 evaluation indexes were selected from six aspects such as water resources protection, shoreline management and protection, water pollution prevention and control, water environment management and ecological restoration, law enforcement supervision and construction of river chief system and its working mechanism. According to the evaluation level and standard of river chief system, the evaluation model of regional river chief system was established based on the cloud model. The combination weight was obtained by AHP and EVM method in this model, and the membership degree of each indicator was got by use of the X conditional Cloud Generator. To avoid the defect caused by maximum subordination principle, calculation was made by weighted average method. The work of river chief system in Nanjing from 2013 to 2017 was evaluated by this model, and get the comprehensive score of assessment which increases gradually, which is basically consistent with the implementation of river chief system in Nanjing, showing that this evaluation model is suitable for the assessment and evaluation of regional river chief system.