The spatiotemporal heterogeneity in the concentrations of atmospheric CO2 and tropospheric O3 is increasing under climate change, threatening food security. However, the impacts of short-term elevated CO2 or O3 on undamaged kernels in rice remain poorly understood, especially the impacts of their combination. We conducted an open-top chamber experiment to examine the impacts of short-term elevated CO2 (+200 ppm, eCO2) and O3 (+40 ppb, eO3) on undamaged kernels in rice cultivars (NJ5055 and WYJ3). We found eCO2 significantly reduced undamaged kernels by 35.2% and 66.2% in NJ5055 and WYJ3, respectively. EO3 significantly reduced undamaged kernels by 52.4% and 47.7% in NJ5055 and WYJ3, respectively. But the combination of eCO2 and eO3 did not affect the undamaged kernels in both cultivars. Moreover, we found that undamaged kernels were significantly correlated with chalky kernels (r = −0.9735). These results highlighted that changes in chalky kernels are most responsible for the changes in undamaged kernels in rice under eCO2 and eO3. This study demonstrated that undamaged kernels in rice are fragile to climate change factors like short-term eCO2 and eO3, and reducing chalky kernels is one of the most important adaptations to sustain food security in the future.