Comprehensive screening of rice (Oryza sativa L. subsp. japonica Kato) germplasm resources with different nitrogen (N) efficiency levels is effective for improving N use efficiency (NUE) while reducing pollution and providing high quality, yield, and efficiency agriculture. We investigated 14 indices of 38 varieties under three N application levels to assess differences among genotypes. Rice varieties were classified for screening and identifying N efficient. Descriptive statistical analysis results indicated significant differences in relative yield, and also in NUE indices (agronomic utilization rate and partial productivity of N fertilizer). The genotype main effects and genotype–environment interaction effects (GGE) biplot analysis was used to evaluate suitable varieties, compare the stable and high yield capabilities of different varieties, find the ideal variety, and describe the correlation, discrimination and representativeness of the indices under different N application levels. Descriptive statistical, discrimitiveness and representativeness and factor analysis were used to select indices, in which the panicle number per plant and soil and plant analyzer development (SPAD) value were the key indices for evaluation and identification. Heatmap and hierarchical cluster analysis based on the average value of evaluation indices, and scatter plot based on the comprehensive value of N efficiency (P) according to formula showed that all varieties could be divided into five types under different N treatments. Our findings work toward developing N efficient rice varieties to improve NUE, reduce N fertilizer application and thus N waste, consequently mitigating the effects of rice production on the environment to ensure food security and sustainable agricultural development.