Exploring the impact of individual capabilities on ecosystem services and farmers’ well-being is conducive to discovering the complex relationship between ESs and human well-being, and has clear practical value for the sustainable management and improvement of farmers’ well-being in ecologically fragile areas in China. An importance–accessibility index of ESs was constructed and the objective well-being and subjective well-being of farmers were assessed. Subsequently, the relationship among capabilities, ESs, and well-being was elucidated based on a structural equation model. The results showed that fruits, pest control, fuelwood, water conservation, and wild food were the ES types that contributed most to farmers’ well-being. There were some similarities and differences between the dimensions of objective and subjective well-being. For example, farmers with adequate leisure time reported higher leisure satisfaction and farmers with relatively adequate income levels reported the lowest income satisfaction. The direct effect of capabilities on ESs and objective well-being was significant, and the direct effect of capabilities on their subjective well-being was not significant. Their capabilities had a significant indirect impact on their objective well-being by influencing ESs and did not have a significant indirect impact on their subjective well-being by influencing ESs; their capabilities had a significant indirect impact on their subjective well-being by influencing the ESs and objective well-being. Physical health, mental health, and agricultural skills were the key types of capabilities that influenced the farmers’ access to ESs and well-being. Improving these capabilities can enable local farmers to more fully access ESs and improve their well-being.