Food safety risk management is an important cross-boundary issue around the world from both theoretical and practical perspectives. Public–public collaboration is the most basic form of cross-boundary governance. This study investigates the main factors affecting the governance effectiveness in public–public collaboration for food safety risk management through a questionnaire survey in Jiangsu Province and Guangxi Zhuang Autonomous Region, China, using a multivariable linear regression model based on principal component analysis. The results show that although the governance effectiveness in public–public collaboration is affected by many factors, the most important of which are the behavior and capabilities of legislative, administrative regulation and enforcement, and environmental improvement government (public) agencies, professionalism of government agencies, and laws and regulations as the basis for government agencies to perform their responsibilities. This research provides a case study for the academic community to better understand the main problems facing public–public collaboration for food safety risk management in China. It also provides insights into promoting public–public collaboration in developing countries.