Two rice cultivars, Wuyunjing23 (WYJ) and IIyou084 (IIY), have a different response to elevated [CO₂] in their seed yield. It is not clear how their seedling root respond to high [CO₂]. In this study, hydroponic culture and agar plate culture were utilized to explore the difference in WYJ and IIY response to elevated C condition in seedling root morphology. The results of hydroponics experiment showed that the elevated [CO₂] increased shoot biomass of IIY by 28.5% under low nitrogen condition, and the dry weight of root was significantly responsive to high [CO₂] at seedling stage. The number of adventitious roots was not increased significantly, and the total root length played a more important role in root biomass response. The total root length of IIY increased by 26.3% under high [CO₂], and the root length in both levels of root diameter had high response. The response of shoot and root biomass of WYJ was not significant under low nitrogen level, while it is not the case under normal and high nitrogen levels. Under normal nitrogen condition, the response of WYJ shoots to high [CO₂] was not significant, while its root biomass was increased significantly by high [CO₂]. The number of adventitious roots was increased by 25.8%, while the total root length was increased by 45.0%. The root length in both levels of root diameter had high response. IIY did not respond significantly under normal nitrogen. At the high nitrogen level, the shoots biomass of WYJ was increased by 35.5% under high [CO₂], the root biomass was increased by 80.3%, the number of adventitious roots was increased by 38.5%, and the root mean diameter was increased by 16.7%. The total root length had no response to elevated [CO₂], and the biomass of IIY had no significant difference under high nitrogen condition. At the same time, WYJ showed higher response in the root surface area and volume to high [CO₂] than IIY under normal nitrogen and high nitrogen conditions. The results of agar plate culture test were consistent with the results of water culture test, and response of WYJ root morphology to high concentration of sucrose was higher than that of IIY. The results showed that the different response to high C condition between cultivars would not change with different culture conditions. Different from the response in middle and late growth stage, response of seedlings root biomass and morphology to high [CO₂] was more significant in WYJ than in IIY at normal nitrogen level, which shows that the response of rice yield are not always consistent with the response of seedling growth. The high response of seedling growth may not reflect the high response of later yield.