The informatization projects funded by special fiscal funds are overseen by multiple departments, which highlights the risks in audit control. This article uses a national-level ministry’s government digitalization project as a case study to systematically identify the causes of audit risks throughout the project lifecycle and build a full-chain supervision and risk control system. It effectively avoids audit risks, standardizes project management processes, and ensures the compliant use and efficient allocation of special fiscal funds. The supervision and risk control model developed can improve the standardization and traceability of government informatization projects, providing practical reference for supervision and risk management of similar fiscal informatization projects.