Previous studies on the efficiency of higher education institutions have generally approached the functions of higher education from a limited perspective, and the studies have followed traditional methods. The aim of this study is to determine the teaching, research, and third mission technical efficiency of universities, to rank efficient universities, to identify potential areas for improvement, and to examine the determinants of efficiency scores and the differences in scores in terms of various variables. In this study, the efficiency of 187 universities was measured by data envelopment analysis. Efficiency criteria were weighted by both objective and subjective multi‐criteria decision‐making (MCDM) methods and ranked by different MCDM methods. Beta and Linear regression were performed to determine the factors on efficiency scores. According to the results of the study, the most efficient universities are in the fields of research, teaching, and third mission, respectively. Budget criterion is the most important input criterion. Number of graduates, number of publications, and number of social responsibility projects are the most important output criteria. Having an older history positively predicts teaching and research efficiency. The size of universities and being located in developed regions negatively predict research and third mission efficiency. There is a positive relationship between rankings in teaching, research, and third mission. This research provides more comprehensive information to universities by considering teaching, research, and third mission efficiency separately. Second, this research proposes a new methodology for higher education efficiency measurement by integrating DEA and hybrid MCDM. Finally, this research provides new insights by analyzing factors related to teaching, research, and tertiary mission efficiency.