AbstractNitrification in the rhizosphere is a crucial process in controlling nitrogen‐use efficiency (NUE) in flooded paddy soils. To understand the relationship between the nitrification ability of the rhizosphere and NUE, pot experiments using 15N tracer technique were conducted to investigate the impacts of the rhizosphere soil net nitrification rate on NUE and denitrification losses at different rice growth stages in two paddy soils, which were sampled from Jurong (JR) and Yancheng (YC) in Jiangsu Province in China. The results showed that the nitrification rate in JR rhizosphere soil was lower than in YC rhizosphere soil at all rice growth stages. The abundance of ammonia‐oxidizing bacteria (AOB), ammonia‐oxidizing archaea (AOA), and pH in YC rhizosphere soils were always higher than in JR rhizosphere soils. Rice yield, biomass, NUE, leaf glutamine synthetase (GS) activity, and nitrate reductase (NR) activity were higher in JR soils with low nitrification rates than in YC soils with high nitrification rates (p < 0.05). In contrast, denitrification loss from JR soil (12.69%–23.41%) was lower than that from YC soil (26.83%–40.98%; p < 0.05) for each rice growth stage. The biomass and NUE decreased significantly as the net nitrification rate, the abundance of AOA and AOB of both the JR and YC rhizosphere soils increased (p < 0.05), and the denitrification loss was enhanced as the rhizosphere nitrification rate increased in the JR and YC soils (p < 0.05) during the rice growth period. The rhizosphere‐dominant AOB community Nitrosospira is the key factor affecting the nitrification rate and then decreasing rice NUE. In general, the rhizosphere nitrification rate in paddy soils is a primary factor controlling the rice NUE and denitrification loss.