The internal reporting system (also known as the whistleblower system) for food safety serves as a vital instrument to compensate for inadequate regulatory capacity by leveraging the information advantage of insiders. However, the institutional inertia of treating whistleblowers as “tools” has led to a path dependence characterized by “prioritizing incentives, neglecting protection, and lacking remedies”. This has plunged the system into a predicament where protection mechanisms are hollowed out, incentive mechanisms are misaligned, and remedy mechanisms are dysfunctional. In response, this article proposes a systematic pathway for improvement, which involves: 1) constructing a robust protection line centered on “absolute confidentiality” and “comprehensive anti-retaliation” to reduce reporting risks ex ante; 2) establishing a precise incentive system based on “high-percentage, uncapped, and rule-based” rewards while optimizing the disbursement process to enhance incentive effectiveness; and 3) setting up dedicated remedy channels and implementing the reversal of the burden of proof to safeguard whistleblowers’ rights ex-post. This integrated strategy seeks to offer practical ideas for empowering internal supervision and fulfilling the system’s original purpose in food safety governance.