Based on the theoretical research of water flow ecological protection and compensation at home and abroad, the connotation of water flow ecological protection and compensation is discussed. The domestic water flow ecological protection and compensation laws, policies and pilot practice are analyzed. It is pointed out that the problems existing in the current process of compensation for water flow ecological protection include the lagging construction of laws and regulations, the imperfection of technical support systems of compensation standards and quantitative evaluation criteria, the single source of compensation funds and means of compensation, the imperfection of supporting basic system, the lack of effective consultation mechanism and platform, etc. Some countermeasures and suggestions are put forward from the aspects of perfecting the policy and regulation system, supporting basic system and standard system, promoting the diversification of compensation fund channels and ways, and straightening out the management system and mechanism.