Canopy temperature can be a good indicator of stomatal conductance. To understand the genetic basis of phenotypic differences in stomatal conductance between average and high-yielding rice (Oryza sativa L.) cultivars, we conducted a quantitative trait locus (QTL) analysis of canopy temperature. We developed reciprocal series of backcross inbred lines (BC1F6) derived from a cross between the average-yielding japonica cultivar ‘Koshihikari’ and the high-yielding indica cultivar ‘Takanari’. A stable QTL, qCTd11 (QTL for canopy temperature difference on chromosome 11) on the short arm of chromosome 11, accounted for 10.4 and 19.8% of the total phenotypic variance in the two lines; the ‘Takanari’ allele decreased the canopy temperature difference value. A chromosome segment substitution line carrying the Takanari qCTd11 showed a greater reduction in canopy temperature than ‘Koshihikari’, and had higher stomatal conductance and photosynthetic rate. These results suggest that qCTd11 is not only involved in canopy temperature, but is also involved in both stomatal conductance and photosynthetic rate.