The watershed ecological compensation mechanism is an important support for the development of ecological civilization in China. Taking the Dongjiang River Basin and the Chishui River Basin as examples，this paper summarizes the practical experience in compensation methods and compensation mechanisms in the course of the pilot construction，and discusses the institutional advantages and bottlenecks of the government compensation mode and the market compensation mode. The paper puts forward some suggestions including pushing forward legislation，promoting the marketlized and diversified development，optimizing implementation plan，to improve the watershed ecological compensation mechanism，which has some reference value to further promote the watershed ecological compensation mechanism in China.