The key ecological function area undertakes important missions to protect and repair the ecological environment and to provide the ecological products. As the most important subject of ecological protection, farmers face the impact of multiple risks. The multi-dimensional perception of risks not only affect their production behavior decisions, but also affect the main functions of key ecological functional areas. Therefore, it is urgent to accurately understand the multi-dimensional perception of farmers' livelihood risks and its influencing factors, so as to provide reference for formulating effective livelihood risk prevention system. This paper selected the Yellow River Water Supply Area of Gannan as study area. Based on 527 households survey data, we analyzed the features of farmers' perception to livelihood risk and its key impact factors by using the econometric model. The results show that:① The family development needs risk, health risk and social risk have been the main livelihood risks which farmers are facing in the Yellow River Water Supply Area of Gannan. The proportion of farmers who face environmental risks, family development needs risk, and policy risks in key conservation zones are significantly higher than those of the farmers in restoration zones and economic demonstration zones. ② Farmers' familiarity perception, voluntary perception and continuance perception of family development needs risk are strong. Farmers' panic perception, severity perception, and probability perception of health risk are strong. Farmers' controllability perception of social risk is strong. The farmers' perception of the controllability of policies risk, markets risk, and health risk in key conservation zones are higher than those in other regions. ③ Human capital has significant direct impacts on probability perception, severity perception, panic perception, and familiarity perception. The physical capital has significant direct impacts on voluntary perception. Finally, we put forward the countermeasures and suggestions for farmers to prevent livelihood risks.