According to the practical issues, such as high repetition, unsmooth data-sharing and poor compatibility between systems in academic papers auditing system of postgraduates, this paper suggests integrating the academic papers auditing system of postgraduates with the universities Institutional Repository. The function module of academic papers auditing system of postgraduates is divided into four modules, i.e. papers-submitted module, academic evaluation module, user management module, and system security module. This paper also analyzes the integration process from process design, database table design and document archiving table design between Institutional Repository and academic papers auditing system of postgraduates. Finally, it proposes some thoughts about construction process of the system integration.