In order to strengthen the audit supervision of scientific research project management, resolve the organizational planning difficulties faced in scientific research project audit, improve the audit coverage and accuracy of audit implementation, establish scientific, unified and standardized audit workflow and standards, and create higher audit value. This paper is risk oriented, starts with the whole process of scientific research project audit. It firstly establishes a matrix audit model, closely focuses on the high-risk areas and key management links of various business flows involved in scientific research projects, accurately benchmarkes. Then, it completes the exploration of the digital audit path of the whole process of scientific research projects, forms a standard operating process, completes the project tasks. Finally, it finds problems and puts forward suggestions, which is of great significance to improving the risk prevention and control and self construction ability of scientific research projects. It plays a good role in promoting independent research and development capability. Through practice and timeliness management requirements, this paper enlightens the thinking of risk oriented agile audit mode for scientific research projects. It has a good reference value for relevant aviation manufacturing enterprises to carry out scientific research project management audit or self construction.