Abstract Increasing concentrations of atmospheric CO2 are projected to have positive effects on crop photosynthesis and yield (CO2 fertilization effect, CFE). High-temperature events, such as heatwaves, during sensitive periods can have significant negative impacts on crop yield and quality; however, the combined effects of elevated CO2 (EC) and short-period elevated temperature (ET) have not been determined in the open field. Here, we show a strong negative interaction between EC and ET obtained from a temperature-free-air controlled enhancement treatment embedded in a season-long free-air CO2 enrichment (FACE) experiment on a japonica rice cultivar, Koshihikari, over three seasons at the Tsukuba FACE facility in Ibaraki, Japan. CFE was 15% at ambient temperature, but it was reduced to 3% by ET, where canopy surface temperature (Tc) was elevated by ∼1.6 °C for 20 d after flowering. Reductions in CFE mainly arose from poor grain setting at Tc above ∼30 °C. High Tc also increased the percentage of chalky grains and substantially decreased the grain appearance quality, although the threshold temperature varied between the seasons. Simultaneous increases in atmospheric CO2 concentration and air temperature are expected to increase daytime canopy temperatures more than air warming alone, thereby affecting grain yield and quality. Crop models without these processes are likely to underestimate the negative impacts of climate change on crop yield and quality. The development of adaptation measures against heat stress, particularly during reproductive and grain-filling periods, needs to be enhanced and accelerated.