Gray system theory is a new field of control theory, which is the product of applying cybernetics and methods to social and economic systems, and is also the product of the combination of control theory and operations research. It takes the gray system as the research object. Whitening, desalination, quantification, modeling, and optimization are the core of the gray system, and it aims to predict and control the development of various gray systems. The purpose of this paper is to study how to analyze and study the impact of higher education cooperation projects with the help of multi-dimensional gray theory and describe the gray system theory. The problem of analyzing the impact of cooperation projects proposed in this paper is based on the gray theory, so it is elaborated around its concept and related algorithms, and a case design and analysis of the impact of higher education cooperation projects are carried out. The experimental results show that the institutions responsible for infrastructure at the top of the school have the greatest impact on infrastructure projects, accounting for about 70%, with 20% weight for communication with government agencies, and about 10% for communication with users.