Higher education management is an important way to cultivate college students' awareness and behavior of ecological environment protection. The survey results show that at present, college students mainly rely on theoretical courses and lectures to receive ecological civilization education, but they lack practical links, which is different from the goal of ecological civilization education. Therefore, this paper comprehensively considers the weight of eco-environmental protection consciousness to higher education management and their relationship by using fuzzy comprehensive evaluation analysis method, which provides scientific basis for relevant decision-making. On the whole, fuzzy comprehensive evaluation analysis method can help to deeply understand the relationship between different factors and provide strong support for promoting eco-environmental protection in higher education management.