Education funds serves as a crucial foundation for the high-quality advancement of education, with fairness and efficiency being the primary metrics for evaluating the effectiveness of higher education funds distribution. This study utilizes data from 2012 to 2019 pertaining to “Double first-class” universities under the Ministry-affiliated Universities. It employs per-student expenditure as an operational indicator for assessing the equitable distribution, while the super-efficiency slacks-based measure (SBM) model is utilized to evaluate the efficiency of education funds allocation. Additionally, the Markov chains model and a comprehensive evaluation model are applied to assess the potential for education funds allocation, thereby identifying opportunities for optimizing Higher education funds. The findings indicate a low level of internal mobility regarding the overall fairness and efficiency, suggesting that significant progress in this area is challenging. Because of the constraints imposed by the original allocation, the issue of “long-term inequality” stands out more prominently than that of “long-term inefficiency.” Furthermore, over 90% of higher education funds exhibit a negative comprehensive evaluation index concerning their allocation potential, with optimal allocation potential primarily driven by equitable distribution. Based on the potential of higher education funds allocation, one may choose to adhere to a path that prioritizes efficiency and focuses on significantly enhancing stable funding, as well as a path that strengthens balanced safeguards and aims for breakthroughs in improving the effectiveness of funding, so as to realize the efficient and equitable allocation of higher education funds.