Two different rice cultivars, Yangdao 6 [Indica rice cultivar with high nitrogen-use efficiency (NUE)] and Nongken 57 (Japonica rice cultivar with low NUE) were used to study the relationship between NUE and nitrification activity in the rice seedling rhizosphere soil using a rhizobox with three compartments, and a soil-slicing method. The roots of both rice cultivars developed aerenchyma tissue [expressed as percentage porosity of root (POR)], but Yangdao 6 showed better development than Nongken 57. This root morphology change results in more radial oxygen loss (ROL) into the rhizosphere. Leaf glutamine synthetase activity (GSA) and nitrate (NO3-) reductase activity (NRA) of Yangdao 6 were significantly higher than those of Nongken 57, while there was no significant difference in root NRA between the cultivars. The nitrification activities were maximal in rhizosphere soil, followed by those in the bulk soil and the root surface for both cultivars. The rhizosphere nitrification activity, NO3- concentration and abundance of ammonia-oxidizing bacteria (AOB) associated with Yangdao 6 were always higher than those of Nongken 57. Therefore, we conclude that the greater N uptake by Yangdao 6 when compared to Nongken 57 can be mainly attributed to the bigger capacity for nitrification in Yangdao 6.