This chapter aims to explore the scientific research competitive advantages of the C9 university alliance in the context of China’s higher education sustainability. Three traditional science disciplines of chemistry, biology, and physics are accessed to explore the scientific research competitiveness (including the quality of published papers, National Natural Science fund investment, international cooperation and national projects), to explore whether C9 alliance, compared to other universities has ample discipline competitiveness, and the possible influencing factors, such as The Clarivate Essential Science Indicators and In Cites Benchmarking & Analytics. This study applies Mann–Whitney U test to compare the difference of scientific research competitiveness between C9 university alliance and non-alliance universities. Findings indicate that C9 alliance universities possess relative competitive advantages not primarily derived from National Nature Fund funding, but rather from discipline strengths accumulated through long-term development. The study suggests that activities related to forming university alliances should be systematically implemented and go beyond superficial measures, including comprehensive cooperation and initiatives across teaching, research, management, supervision, school construction, and joint projects.