Differences and relative mechanisms of nitrogen (N) uptake efficiency between indica-japonica hybrid rice, namely Yongyou 12 (YY-12) and Jiayouzhongke 6 (JY-6), and conventional japonica rice, namely Xiushui 134 (XS-134) were studied at low and middle N levels during tillering stage by pot and hydroponic experiments. The results showed that N uptake efficiency of YY-12 and JY-6 were significantly higher than that of XS-134 at both N levels. YY-12 and JY-6 developed significantly greater amount of root biomass compared with XS-134. Moreover, larger porosity of root (POR) was found in YY-12 and JY-6 which produced larger root radial oxygen loss (ROL), thus, probably resulted in larger amounts of ammonia oxidizing bacteria (AOB), much higher nitrification activities and mineral N concentrations in rhizosphere soils of YY-12 and JY-6. The mineral nitrogen concentration in rhizosphere soil was significantly and positively correlated to N uptake efficiency of rice plant. Therefore, the high N uptake efficiencies of YY-12 and JY-6 might be closely related to the increase of nitrification activity and the intensification of organic N mineralization in rhizosphere soil. In addition, YY-12 and YY-6 showed significant higher N uptake efficiency under low N level compared with that under middle N level while XS-134 had no difference, the probable reasons were that the root biomass accumulation and increased proportions of POR of YY-12 and YY-6 were much higher than XS-134 under low N level compared with middle N level, furthermore, the decreased proportions for ROL, nitrification activity and mineral nitrogen concentration in rhizosphere soil of YY-12 and YY-6 were less than that of XS-134.