In recent years, the investment amount of university engineering construction has been increasing significantly, and the establishment of scientific and reasonable cost management system has become particularly important in the investment control of engineering construction. This paper explores the investment control of university engineering construction and designs the basic framework based on three parts: whole process cost control, full caliber cost audit and full gradient grading management. With the help of BIM, we build a cost management system, which is divided into the planning stage, bidding stage, mid-construction, until the completion of the collation of cost data, extraction and preservation of cost indicators. After establishing a full range of cost management systems, the adjacency matrix X algorithm and functions are used to calculate. The experiment proves that: the investment estimate before the project construction affects more than 75% of the overall investment, and the all-round cost management system built based on BIM can make the investment estimate accurate and stable at 75%, and the negotiation change rule based on this is to save nearly 25% of the investment funds. The comprehensive cost management system has a comprehensive and detailed grasp of the cost process of specific construction projects and specific issues during construction, fully protecting the university’s investment interests.