As one of the main scenarios of future climate change, studies have shown that high atmospheric concentration CO₂ ([CO₂]) will promote rice yield and the yield increase varies greatly between two rice subspecies (indica and japonica). However, there is still a knowledge gap on whether the yield response difference between subspecies is related to root growth. Here we conducted a FACE (free air CO₂ enrichment, FACE) experiment using “weak” (Oryza sativa L. japonica, Wuyungeng 23) and “strong” (Oryza sativa L. indica, Yangdao 6) yield responsive varieties, elevated [CO₂] (590 μmol/mol) and control (390 μmol/mol) treatments were set. Minirhizotrons were used to detect the root growth status of the two varieties continuously and dynamically, and the root turnover rate was further calculated. The results showed that elevated [CO₂] significantly enhanced the growth of rice roots of the two varieties, and the root length, surface area and volume across two varieties were increased by 120%, 106% and 98% on average compared to the control, respectively. The root turnover rate of Wuyungeng 23 was significantly reduced by 66% under elevated [CO₂], the root turnover rate of Yangdao 6 increased by around 18%. For Wuyungeng 23, most of the root increased by elevated [CO₂] was mainly distributed in the shallow layer (32% to 56%), however, the root distribution of Yangdao 6 in the deep layer was increased from 12% to 20% by elevated [CO₂]. Combination with the yield response and aboveground nitrogen uptake, we concluded that compared to root morphological indicators such as root length, the turnover rate of rice root system and the distribution ratio of deep root system may be the main reason for the obvious difference in the response of indica and japonica rice to elevated [CO₂].