Frequent accidents in fresh agricultural product supply chain have brought huge losses to China’s farmers.Based on the analysis on the features of emergency in fresh agricultural product supply chain, this paper divides risk of farmers into three types in accordance with the sources of emergency: natural risk, market risk and production risk and puts forward such problems as lack of emergency response capabilities and methods, narrow access to information, and limitation of resources and configuration capability. Finally, from the perspective of supply chain network,three kinds of emergency modes are put forward , including the combination of government and farmers, horizontal alliance and longitudinal alliance of supply chain, in order to improve the effectiveness of emergency management and reduce farmer’s losses caused by emergencies.