In recent years, higher education management has been improving, but the coordinated development of the overall educational management and student management system of colleges and universities still needs to be further improved and enhanced. This paper uses data envelopment analysis and data fusion technology to establish DEA fusion algorithm and DEA-Malmquist index method to evaluate and analyze students’ learning efficiency in colleges and universities. The results indicated that the average degree of perfection of online teaching management in higher education is low, 86.2%. Students’ overall satisfaction with this is also expected at 56.2%. There is a need to strengthen management and improve classroom interactivity and innovation, to enhance the quality and attractiveness of courses, and to avoid excessive fragmentation. In addition to the existing problems, the results achieved include more accessible access to learning resources, with a percentage of 88.6%. The algorithm of this paper is used to study the efficiency of higher education and student learning, and to provide a more comprehensive and objective approach to the development of the quality of higher education and student management for the later development of higher education.