With the implementation of numerous ecological restoration projects, the vegetation cover in South China Karst has significantly improved. However, especially in rural areas, local farmers' perceptions of vegetation (FPV) have not yet been systematically studied. The farmers' attitudes and perceptions can directly influence the sustainability and effectiveness of ecological restoration. FPV is prone to bias, and understanding this bias is important for promoting farmers' active participation in ecological restoration. Focusing on the FPV bias, this study quantified the subjective and objective values of vegetation through questionnaires (n = 677) and the normalized difference vegetation index from Huanjiang County, China. Concurrently, the current status of vegetation cover (CVC) and vegetation change over the past (VCP) were jointly incorporated into the analysis. It was found that farmers' perception of CVC was more accurate than that of VCP. Overall, CVC perception was mostly positively biased, while VCP perception was slightly negatively biased. Mutual information analysis further revealed that FPV was more strongly associated with CVC (0.064) than with VCP (0.02). Notably, in areas with poorer vegetation cover, FPV significantly exceeded actual CVC, possibly because economic and social prosperity compensated for the scarcity of vegetation. In addition, there were significant differences in the FPV bias across individuals and geographic characteristics. The mediating analysis showed that CVC exerted a significant direct effect on Bias-CVC (beta = -0.578, p < 0.01), while VCP had no significant direct effect on Bias-VCP. In addition, social well-being, environmental value orientation, and social influence indirectly affected Bias-CVC. The study suggest that, in karst areas with prominent rocky desertification, understanding of the perceptual needs of farmers can optimize the layout and mode of ecological restoration projects, effectively improving the well-being of farmers.