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Extremely high air temperature at the heading stage of paddy rice causes a yield reduction due to the increasing spikelet sterility. Quantifying the damage to crops caused by high temperatures can lead to more accurate estimates of crop yields. The remote sensing technique evaluates crop conditions indirectly but provides information related to crop physiology, growth, and yield. In this study, we aim to assess the crop damage caused by heat stress in paddy rice examined under elevated air temperatures in a temperature gradient field chamber from 2016 to 2019, using remote-sensed vegetation indices. A leaf-spectrometer, field-spectrometers, and a multi-spectral camera were used to monitor the conditions of paddy rice. Although, in the leaf- and canopy-scales, the values of normalized difference vegetation index (NDVI) and photochemical reflectance index (PRI) decreased after the heading of rice under normal conditions, the decreasing sensitivity of NDVI and PRI was different depending on the degree of physiological heat stress by high temperature conditions. The NDVI after the heading under extremely high air temperature was not dropped and remained the value before heading. The PRI decreased at all air temperature conditions after the heading; the PRI of the plot exposed to the elevated air temperature was higher than that under ambient air temperature. Further, the relative change in NDVI and PRI after the heading exhibited a strong relationship with the ripening ratio of paddy rice, which is the variable related to crop yield. These remote-sensing results aid in evaluating the crop damage caused by heat stress using vegetation indices.