Among the essential plant nutrients, nitrogen (N) is the most important and universally deficient in rice cropping systems worldwide. Despite different practices available for improvement of N management, nitrogen use efficiency (NUE) is still very low in rice, particularly under conventional management practices. This study was conducted to assess the effect of two crop management practices including the system of rice intensification (SRI) versus conventional management practices (CP) with four N application levels (60, 90, 120, and 150 kg N ha) and absolute control (i.e., without N application) on rice growth, grain yield, and NUE. Experiments were established in split-plot randomized complete block design in three replicates. Crop management practices and N levels were treated as the main effect of main-plots and sub-plots, respectively with replicate blocks treated as random factors. Results indicated that deploying of SRI increased rice grain yield by 17.5 and 52.4% during wet and dry seasons, respectively compared with the CP. Rice grain yield was significantly (p < 0.05) higher in SRI than in CP at all levels of N application compared. The application of N at 120 and 60 kg ha resulted in the increase in rice grain yields by 49 and 46.5%, respectively, relative to the absolute control during wet and dry seasons. Nitrogen application had a significant effect (p < 0.05) on agronomic nitrogen use efficiency (ANUE) and partial factor productivity (PFP). Results also indicated that agronomic nitrogen use efficiency (ANUE) was higher (27.2 kg grain kg N) during the wet season with an application of 60 kg N ha. Furthermore, higher ANUE (23.8 kg grain kg N) was recorded during dry season with an application of 90 kg N ha. The significant (p < 0.05) interaction effects of treatments were recorded on PFP between SRI and 60 kg N ha during the wet (116.7 kg grain kg N) and dry (105.8 kg grain kg N) seasons. This study revealed that ANUE and PFP decreased with N application at the levels of 120 and 150 kg N ha under SRI and CP during the two cropping seasons. The findings of the present study provide potential information that rice grain yield and higher NUE could be achieved at low N inputs under SRI, and thus reducing costs resulted from fertilizer inputs without compromising other environmental benefits.