Exploring the relationship between the livelihood capital of farmer and well-being is significant for improving the well-being of farmer in ecologically fragile areas and effectively reducing poverty. This study takes Dujiashigou of Mizhi County, Shaanxi Province as an example, which is located in the loess hilly and gully region. Through the constructed index system, the status quo of farmers' livelihood capital and well-being were analyzed, and the Structural Equation Model was used to explore the impact of farmers' livelihood capital on their well-being and its group differences. The results show that: ① the overall livelihood capital of farmer shows a spatial layout of "low value dispersed, high value concentrated", and there are significant spatial differences in the livelihood capital of different farmer groups. ② The spatial distribution pattern of objective well-being of farmers as a whole is "scattered at low values and locally clustered at high values", and the spatial distribution pattern of subjective well-being is "high around and low in the middle"; there are significant differences in the spatial distribution of subjective and objective well-being levels among farmer groups. ③ Farmers' overall livelihood capital has a significant positive effect on well-being and objective well-being on subjective well-being, and there are significant differences in the effects of each sub-dimension of livelihood capital on farmers' well-being. ④ There are group differences in the effects of farm households' livelihood capital on well-being, pure agricultural farmers improved well-being through housing status, crop type and actual cultivated area per capita; crop type, housing status and linkage costs contributed more to part-time farmers; while household fixed assets, male labor force ratio and average age of household head mainly affected non-agricultural farmers. The study offers promising methods and approaches for improving the well-being of specific farmer groups.