E-government is an important foundation for realizing the national informatization strategy. In the era of big data, e government cloud security is faced with severe challenges. Data leakage, account hijacking, system vulnerability and other factors hinder the development of government informatization. Error detection and correction are the basic responsibilities of auditing. As a means of supervision, cloud security auditing effectively caters to the security management and control requirements of e-government cloud. Faced with the complexity of cloud computing, how to establish a set of mature e-government cloud security audit strategy system has become a hot issue to be solved urgently. On the basis of theoretical review, this paper designs the framework of e-government cloud security audit, determines the audit mode and technology methods of e-government cloud security, analyzes the composition of e-government cloud security audit risk, explores the e-government cloud security audit mechanism based on the modules of infrastructure security, data information security, application service security, security organization management, and generates a feasible and scientific e-government cloud security audit system. The research conclusions of this paper provide theoretical support for the security management practice of e-government cloud in the era of big data from an audit perspective, and provide a practical reference for the construction of e government cloud security audit strategy.