In warm and humid Holocene Japan, continuous human intervention has been essential for maintaining grasslands. Rural agricultural landscapes harbor seminatural grassland habitats, such as meadow and small-scale paddy levees. For the past half-century, many rural settlements have been abandoned due to changes in the industrial structure and the rural-to-urban shift of the human population, resulting in rapid degradation of seminatural grassland habitats. To examine how land abandonment affects community assembly in relation to species traits, we surveyed butterfly occurrences in abandoned and inhabited rural settlements across 18 regions in Japan. We estimated species-specific sensitivity to land abandonment and the dependence of the sensitivities on species' niche characteristics. Although the dominant vegetation in abandoned settlements was grassland, grassland butterflies declined the most due to land abandonment. The butterflies that prefer cool temperatures were negatively affected by land abandonment. These results indicate that land abandonment results in the loss of relict species adapted to the Pleistocene cold climate. As an application of our study, we created a map of priority sites for other effective area-based conservation measures (OECMs) that minimize the negative impact of land abandonment on the butterfly community. Conservation of agricultural landscapes will be an effective measure for climate change adaptation, mitigating the negative effects of global climate change on organisms through small-scale countermeasures.