It is of great significance to study the root characteristics of rice to improve water and nitrogen (N) use efficiency and reduce environmental pollution.  This study investigated whether root traits and architecture of rice influence grain yield, as well as water and N utilization efficiency.  An experiment was conducted using the upland rice cultivar Zhonghan 3 (a japonica cultivar) and paddy rice cultivar Huaidao 5 (also a japonica cultivar) using three N levels, namely, 2 g urea/pot (low amount, LN), 3 g urea/pot (normal amount, NN), and 4 g urea/pot (high amount, HN), and three soil water potentials (SWPs, namely, well-watered (0 kPa), mildly dried (–20 kPa) and severely dried (–40 kPa).  The results showed that with decreasing SWP, the percentage of upland rice roots increased in the 0–5 cm tillage layer, and decreased in the 5–10 and 10–20 cm tillage layers, whereas paddy rice roots showed the opposite trend.  With increasing amounts of N, the yield of upland and paddy rice increased, and the percentage of root volume ratios of the two rice cultivars in the 0–5 and 5–10 cm tillage layers increased, whereas that in the 10–20 cm tillage layer decreased.  The roots of upland rice are mainly distributed in the 10–20 cm tillage layer, whereas most paddy rice roots are in the 0–5 cm tillage layer.  These results indicate that the combination of −20 kPa SWP and NN in upland rice and 0 kPa SWP and LN in paddy rice promotes the growth of the root system during the middle and late stages, which in turn may decrease the requirements for water and N fertilizer and increase rice yield.