The rising of atmospheric carbon dioxide (CO₂) concentration has been blamed for global warming, but it promotes the leaf photosynthesis of crops because CO₂ is the main substrate for photosynthesis. In order to understand the effect of elevated CO₂ concentration on diurnal courses of CO₂ uptake of hybrid rice, a paddy field experiment utilizing free air CO₂ enrichment (FACE) technology was undertaken to determine diurnal courses of leaf photosynthesis at heading and middle grain filling stages, and its association with the final productivity of rice at maturity. Two hybrid rice variety Yongyou 2640 (YY 2640) and YLiangyou No.2 (YLY 2) were grown in the ambient CO₂ and the elevated CO₂ concentration (200 μmol/mol above ambient) from plant transplanting until grain maturity. Elevated CO₂ concentration significantly increased net photosynthetic CO₂ assimilation of flag leaves of two hybrids by 52% on average at heading, but the enhancement was reduced to half at the middle grain filling stage. This photosynthesis acclimation was more pronounced in YLY 2. Elevated CO₂ concentration significantly decreased stomatal conductance of two hybrids at both heading and grain filling stages, resulting in lower transpiration and higher water use efficiency. Greater CO₂ responses of leaf transpiration and stomatal conductance were observed in the morning for YLY 2, but YY 2640 showed higher CO₂ effects in the afternoon. Growth at elevated CO₂ concentration significantly increased intercellular CO₂ concentration, but had no clear effects on the ratio of intercellular to air CO₂ concentration and stomata limitation value, and the same trend was observed for the two varieties. The CO₂ effects on the above-ground biomass and its components were greater in YY 2640 than YLY 2, and it was reflected in the significant CO₂ by variety interactions. The results indicated that compared with YY 2640, the lower CO₂ gain on final productivity of YLY 2 might result from photosynthesis acclimation at the late growth stage, and this down-regulation in leaf photosynthesis was not caused by stomatal limitation.