We evaluated the impacts of historical land-use changes (LUCs) from 1987 to 2006 on surface warming rates and rice yields on the island of Shikoku, Japan. We performed two types of numerical simulations (with historical LUCs and with fixed land uses) using a regional atmospheric model (JMA-NHM) and a large-area rice-growth model (PRYSBI). During our study period in Shikoku, the area of paddy fields decreased markedly and the area of building lots and roads increased. Our evaluation suggests that these LUCs caused warming rates in and around paddy fields that were five times those in and around other land uses. The simulated rice yield in 2006 was 0.27% lower (0.012 t ha−1) than in 1987 in response to the change in thermal and solar radiation conditions. These results suggest that decreases of crop yield due to environmental deterioration will be found in other regions where similar LUCs are occurring.