In order to analyze the factors affecting the level of the ecological compensation mechanism and improve the efficiency of ecological compensation in the river basin, on the basis of document sorting and analysis, the 18 influencing factors that affect the ecological compensation efficiency in the river basin are summarized and analyzed based on the system dynamics model. The research uses VENSIM software to conduct model simulation analysis, conduct sensitivity analysis on the input changes of each influencing factor, and obtain the influence of each factor on the overall level of the system. The factors are divided into key, important and secondary levels according to the impact strength, and the countermeasures and suggestions for the establishment of the compensation mechanism are put forward respectively.