The aim of this study is to design an efficient and reliable university fee and financial management system, which adopts a four-layer structure design, including a presentation layer, business logic layer, persistence layer, and data layer, to address the complexity and business requirements of the system. In terms of system function design, the focus is on building the charging module, salary management module, and cashier management module, ensuring the efficient operation of core functions such as tuition collection, faculty salary payment, and financial report generation. In addition, the system also integrates advanced hardware configuration and software environment, for example, using IBM X3850 server and MySQL database management system, to enhance data processing ability and the user experience. Through strict test, the system in terms of functionality and performance to achieve the intended target, effectively improve the efficiency and accuracy of the university financial management. The research results indicate that the system design is reasonable and can adapt to the diverse needs of financial management in universities, providing a modern and automated financial management solution for universities.