Biological nitrification inhibitor (BNI) can play an important role in inhibiting nitrification and enhancing nitrogen use efficiency (NUE) in agriculture. However, most of current BNI studies have been conducted under hydroponics. Variations in genotype-mediated inhibition of soil nitrification are still unknown. In this study, two rice genotypes, i.e. Wuyujing 3 (WYJ3) and Wuyunjing 7 (WYJ7), which were reported to have weak and strong BNI capacity under hydroponics, respectively, and four soils with different pH (i.e. JX (pH 5.09), FJ (pH 6.00), SC1 (pH 7.96) and SC2 (pH 7.94)) were selected. N uptake rates (esp. NH4+ uptake, UNH4), soil N transformation rates and NUE were quantified by 15N tracing experiment to assess the effects of rice genotypes on nitrification inhibition activity. Results showed that rice genotypes with high BNI exudation (i.e. WYJ7) had lower autotrophic nitrification rate (ONH4) and higher UNH4 in rhizosphere compared to WYJ3. ONH4 in WYJ7 reduced by 0.05, 0.42, 1.14, and 0.48 mg N kg− 1 d− 1 compared with WYJ3 for JX, FJ, SC1 and SC2, respectively. Abundance of AOB in soils planted WYJ7 was lower than WYJ3, which was the key factor affecting ONH4. NUE of WYJ7 was higher than WYJ3, although difference between genotypes was not significant. NUE was negatively correlated with ONH4 (P < 0.05). Our results indicated that some rice genotypes can optimize their N acquisition by regulating soil N transformations (particularly nitrification). Developing rice genotype with strong BNI exudation capacity could be a suitable management practice to increase NUE and yield.