Abstract Increased rice yields due to rising atmospheric carbon dioxide (CO 2 ), known as the CO 2 fertilization effect (CFE), is one of several important factors sustaining global food security. However, model projections on future rice yields are still largely uncertain, partly owing to the lack of how CFE varies between rice species. Here, through synthesis of hundreds of field observations, we found the experimental evidence of a 12.8 ± 0.8% yield increase per 100 ppm CO 2 increase for Indica, but only about a half for Japonica (6.3 ± 0.5 %). After accounting for differences in sub‐species, crop model projections showed substantial regional discrepancies of CFE, which are not captured by original models. More importantly, the spatial and temporal variations of rice yield were projected more accurately after considering this sub‐species difference. Together, these results suggest strong influences of genotype on rice yield responses to CO 2 and highlight the need for crop models to consider genotypes for improving projections of global crop yield.