Mechanical transplanting with bowl-type nursery tray (MTB) is a new mechanical cultivation approach to obtain high-yield and superior-quality rice. However, the precision of nitrogen (N) management regimes for obtaining high-yield and good-quality medium indica hybrid rice in MTB is unclear. Therefore, field experiments were conducted with five N application amounts for two medium indica hybrid cultivars in MTB in three studied years. The results indicated that the highest grain yield reached 10.40–12.27 t ha−1 when the N application amount was increased to approximately 245 kg ha−1 across cultivars. In addition, increasing the N application rate significantly decreased the eating quality of both cultivars in the three years in MTB (P < 0.05). The intersections of “high yield” and “good quality” were found at the site with 90% of the maximum yield and optimal eating quality. The corresponding N application amount was 130–140 kg ha−1 across cultivars and years. Critical nitrogen concentration (Nc) models based on total dry matter (TDM), stem and sheath dry matter (SDM), and leaf area index (LAI) had higher fitting precision and predictive abilities for the N content of rice plants (R2 >0.9) than the Nc model based on leaf dry matter (LDM) in both cultivars. However, the stability was poor among the different study years for the nitrogen nutrition index (NNI) calculated using NcTDM compared with those calculated using NcSDM and NcLAI. The reliable NcSDM and NcLAI models were expressed as Nc= 1.97SDM−0.42 (R2 =0.91;RMSE=0.11;n-RMSE=8.94%) and Nc= 3.72LAI−0.34 (R2 =0.93;RMSE=0.37;n-RMSE=15.54%) for medium indica hybrid rice in MTB. The yield increased linearly with NNI from 0 to 0.99 before heading and from 0 to 0.88 at heading in both cultivars. The yield did not increase further with increasing NNI when NNI reached the upper threshold value. However, increasing NNI significantly decreased eating quality (P < 0.05). Finally, the lower threshold value of NNIs obtained 90% of the maximum yield and optimal eating quality were recommended as 0.94, 0.96, 0.90, and 0.80 at the late stage of tillering, initial booting, middle stage of booting, and heading, respectively. This study provides important theoretical references for precise N management of medium indica hybrid cultivars in MTB.