With global warming, pesticide abuse, exotic pest invasions, and other factors, China's agricultural pests and diseases are increasing rapidly every year. The social disaster management system is composed of many farmers, cooperative organizations, and agricultural enterprises, which is fundamental for biological disaster management systems. However, there are some problems are necessary to overcome, such as small scales, scale decentralization, and ineffective management. Harmful organisms are public goods with externality characteristics, and the decentralized management of China is not conducive to their unified prevention and control. Presently, there are limited studies about the impact of agricultural organization on pest prevention and control. Based on the complexity of pest management in China, this review discusses methods and models of risk management of different agricultural organizations(governance structures), pest risk assesment and management by summarizing the research progress of agricultural organization risk management, and pest risk management. In future research, we should determine the effect of different agricultural governance structures on harmful organism control, factors affecting economic loss caused by harmful organisms, and participation of different agricultural organizations in the "unified prevention and control" of harmful organisms. Through the reform of agricultural organizational controls and their systems, the prevention and control efficiency of harmful organisms would be enhanced to provide a necessary reference for relevant government departments to make more effective decisions.