Over time, the relative effects of elevated [CO2] on the aboveground photosynthesis, growth and development of rice (Oryza sativa L.) are likely to be changed with increasing duration of CO2 exposure, but the resultant effects on rice belowground responses remain to be evaluated. To investigate the impacts of elevated [CO2] on seasonal changes in root growth, morphology and physiology of rice, a free-air CO2 enrichment (FACE) experiment was performed at Wuxi, Jiangsu, China, in 2002–2003. A japonica cultivar with large panicle was exposed to two [CO2] (ambient [CO2], 370 μmol mol−1; elevated [CO2], 570 μmol mol−1) at three levels of nitrogen (N): low (LN, 15 g N m−2), medium (MN, 25 g N m−2) and high N (HN, 35 g N m−2). Elevated [CO2] increased cumulative root volume, root dry weight, adventitious root length and adventitious root number at all developmental stages by 25–71%, which was mainly associated with increased root growth rate during early growth period (EGP) and lower rate of root senescence during late growth period (LGP), while a slight inhibition of root growth rate occurred during middle growth period (MGP). For individual adventitious roots, elevated [CO2] increased average length, volume, diameter and dry weight early in the season, but the effects gradually disappeared in subsequent stages. Total surface area and active adsorption area per unit root dry weight reached their maxima 10 days earlier in FACE vs. ambient plants, but both of them together with root oxidation ability per unit root dry weight declined with elevated [CO2] during MGP and LGP, the decline being larger during MGP than LGP. The CO2-induced decreases in specific root activities during MGP and LGP were associated with a larger amount of root accumulation during EGP and lower N concentration and higher C/N ratio in roots during MGP and LGP in FACE vs. ambient plants. The results suggest that most of the CO2-induced increases in shoot growth of rice are similarly associated with increased root growth.