The efficiency of financial governance is critical to the performance and sound development of universities in China. The rational allocation of financial rights is the fundamental cornerstone and important content for achieving efficient financial governance. This paper innovatively analyzes the revenue and expenditure items listed in the publicly issued final statements of universities, and finds that the allocation of financial power in China’s universities is changing, which is reflected in the obvious increase in both revenues and expenditures, decrease in state appropriations and increase in energy-saving and external exchange expenditures. The changes disclose the constantly increasing complexity of the allocation of financial rights in universities and the urgency to optimize the allocation of financial power. From the micro and macro view, this paper systematically reveals the main defects in system construction and joint governance faced by China’s universities, including: (1) implicit relevant provisions made by the Ministry of Education, late published budgets within the universities, lack of communication between departments (faculties) during the university-level budget-making process and imperfect social supervision mechanisms during the university-level budget-implementation process, (2) loosely grouped interest-related parties and the unbalanced management power of the internal parties. To detect the underlying reasons, this paper further analyzes the relevant policies and management modes then summarizes the reasons into three categories: fuzzy policy orientation, unclear role of financial appropriation and insufficient administrative effectiveness. Aiming at tackling the above-mentioned problems that hinder the allocation and implementation of financial rights in China’s universities, this paperformulatesoptimization strategies of financial rights allocation regarding the following three aspects: (1) Through strengthening the budget function and consolidating the budget preparation process, the universities are urged to discover potential problems independently. At the same time, through providing active feedback to governments at all levels and the education sectors, the universities will be able to make policy orientation clear, and further urge the government to function well in the development of universities; (2) Through performing active network governance, universities can clarify the relationship between themselves and interest-related parties as well as the relationship between departments (faculties) within the universities, which will provide the basis for broadening the source of funds; (3) Through adopting the responsibility center management method, universities can clarify the rights and responsibilities between various departments (faculties) within the university, and further promote the balance of allocation of financial rights. These optimization strategies are of practical significance for optimizing the allocation of financial rights in universities, improving financial governance and raising the efficiency of fund management, which thus will enable the authorities to play a better role, the universities to function better and the output of education to be more fruitful. If the problems existing in the allocation of financial rights are effectively solved, universities will be able to coordinate financial rights and authority to a greater extent. In addition, the efficiency of fund utilization and the performance of operating universities will be improved. As a result, the society will be more harmonious. This will help universities in our nation to better support the performance of innovation-driven development strategy, serve the economic and social development, promote excellent traditional Chinese culture, cultivate and practice core socialist values, promote the development of higher education connotation, and assist early realization of the goal of constructing ″a Powerful Nation of Higher Education″.