In order to understand the design of inland free trade zone operation management information system, a research on the design of inland free trade zone operation management information system based on big data platform is put forward. Firstly, this paper analyzes the use of big data analysis tools to comprehensively reform and innovate the operation and development model of government and enterprises in the free trade zone with three application platforms: public information service platform, comprehensive trade business platform and comprehensive supervision platform. At the same time, it puts forward feasible solutions to the problems of talents and funds. Secondly, it describes the construction of the audit mode of inland free trade zone under the background of big data. The free trade pilot zone is an important strategic measure of the country, focusing on institutional innovation, and it is an important way for the country to try first and form a development experience that can be popularized. Finally, the safeguard measures of the audit mode of inland free trade zone under the background of big data are summarized. Applying big data technology to the construction of the audit mode of inland free trade zone is not only in line with the requirements of the times and technological development, but also an important measure to promote the benign development of inland free trade zone.