China's compartmentalized food safety supervision and administration system has long been blamed for recurring food safety incidents. In response, the State Council launched a major institutional reform that aimed to realize whole-chain-based food safety supervision and administration, to strengthen grassroots capacity and to adapt to a society that is complex, risk prone, open and pluralistic. According to the State Council's mandate, the institutional restructuring at various local levels should have been completed by the end of 2013. However, there have been no systematic, open evaluations that have examined progress, effectiveness or effects. This study attempts to explore issues concerning evaluation of the institutional reform: how to understand the role of evaluation in the policy cycle? What are important evaluation questions in different phases of the policy cycle? How to identify evaluation priorities? Specifically, a target group effectiveness evaluation framework was established and applied in Guangzhou city to assess how local government departments responded to the three principal mandates of the State Council’s reforms: integration of mechanisms and functions, integration of resources, and the enhancement of regulatory capability. The results show that such an evaluation framework is a valid way to examine the main goals and components of the reform, but that the indicators and evaluation criteria need be made more context-specific.