In recent years, there have been frequent cases of damage to the ecological environment, and the public interests of members of society have been repeatedly violated. The safety of the ecological environment is worrying. This paper uses the association rule algorithm and fuzzy comprehensive evaluation method to improve the management of the ecological environment damage compensation system. This article has deeply studied the role of association rules in data mining and practically improved them and applied them to the management of the compensation system for environmental damage. This article also constructed a fuzzy comprehensive evaluation model, following the principles of innovation, responsibility, judicial, and openness, clarified the fuzzy comprehensive evaluation and evaluation process, established a set of comments on the evaluation object, determined the membership function, and constructed the damage factor and multiple index factors such as compensation factor and damage object. Based on the use of the improved correlation algorithm, the accuracy and complexity of the model have been improved, reaching 85.47 and 76.32 points, respectively. It is hoped that the research in this article can contribute a little to accelerating the establishment of my country’s ecological environment damage compensation system, safeguarding the interests of the ecological environment, and protecting the ecological environment.