Under the background of insufficient scientific research funding, evaluating the level of scientific research from the perspective of sustainable development is necessary. The study aims to develop an evaluation index system based on the theories for sustainable competitive advantage (SCA), which could be used to evaluate the sustainable development trend of scientific research in universities. In this study, 42 world-class universities in China are used as examples to calculate their SCA performance in scientific research using the entropy and equal weights methods. The scores of scientific research in different universities in the Academic Ranking of World Universities (ARWU) in 2021 are used to verify the effectiveness of the evaluation index system. The results show that the evaluation index system can effectively predict the scientific research performance of universities in the future. It could be deduced from the results that universities with better scientific research performance meet the needs of the external market better and have more valuable, rare, imitable, and ambiguous resources but a lower level of scientific research dynamic ability. The evaluation index system makes up for the lack of emphasis on the potential scientific research capacity of the university in the current evaluation methods. It can help university administrators formulate relevant scientific research management regulations.