Although the financial transfer payment of the national key ecological functional zones covers all regions in China, the compensation funds remain in the necessary ecological restoration costs and basic public services. There is a lack of attention to the willingness of peripheral farmers to receive compensation. In this paper, based on survey data of 553 farmers in the Altai mountain forest grassland ecological functional zones, contingent evaluation method and Heckman two-stage selection model were used to analyze the farmers' willingness to participate in ecological compensation, compensation level, and influencing factors, which could provide a reference for the national key ecological functional zones to introduce ecological compensation policies for farmers. The results showed that:(1) 85.53% of the farmers in the survey area had strong demand for compensation, which was based on the difference of livelihood, income level, and river basin. After adjustment by Heckman expected value estimation method, the farmers' compensation level was 1250.5 yuan/(household · year). (2) Per capita cultivated land area in natural capital had a positive impact on the willingness to participate in compensation and the level of compensation, and Per capita grassland area significantly positively affected the compensation level of farmers. The proportion of labor in human capital had a positive effect on the compensation level of farmers. In material capital, There was a significant negative correlation between the number of livestock stocks and the compensation level, while productive tools had a positive effect on participation intention and compensation level. The total household income in financial capital significantly negatively affected the compensation level of farmers, and whether it was poverty alleviation to consolidate household status had a positive impact on farmers' willingness to participate in compensation. There was a significant positive correlation between Chinese proficiency and farmers' participation intention in social capital, and whether they often went to village-level cultural centers had a positive effect on farmers' compensation level. (3) In ecological perception, the change of rainfall frequency had a significant negative effect on farmers' participation intention and compensation level. The change of water source flow and the importance of forest were negatively correlated with the compensation level of farmers. There was a significant positive correlation between grassland importance and farmers' participation intention. Among individual characteristics, age and gender had significant negative effects on the compensation level of farmers. The householder status had a significant positive influence on the compensation level of farmers. Therefore, in order to obtain extensive support from peripheral micro interest groups for the national key ecological functional zone policy, from the perspective of livelihood capital, we should dynamically monitor the losses of farmers caused by the intensity of prohibition of priority protection units and key control units, and formulate compensation standards based on this. We will accelerate the introduction of a compensation plan for farmers' livelihood restrictions in the Altai Mountain forest and grassland ecological functional zones.