To optimize both grain yield and quality of low-glutelin rice cultivars under N-fertilizer strategies, two-year field experiments involving three low-glutelin rice cultivars (W1240, W1721, W025) and an ordinary rice cultivar (H9405) with five N treatments were carried out to determine the effects of N application rate and genotype on protein fractions contents and Glutelin/Prolamin ratio (Glu/Pro). The difference of protein fraction concentrations affected by N application rate existed in genotypes. Ordinary rice cultivar had a larger increase in glutlein concentration affected by N application rate than low-glutelin rice cultivars did. Glutelin in H9405 had a increase of 30.6 and 41.0% under the N4 treatment (360 kg N ha–1) when compared with N0 treatment (no fertilizer N) in 2010 and 2011 respectively, while all the low-glutelin rice cultivars showed relatively smaller increases for two years. Variance analysis showed no significant effect of N application rate on glutelin in W1240 and W025 while the effects on albumin, globulin and prolamin were significant in low-glutelin rice. What’s more, N treatment had no significant influence on Glu/Pro ratios in low-glutelin rice cultivars while a significant increase in Glu/Pro ratio was observed in ordinary rice cultivar. So low-gultelin rice cultivars showed a different pattern from ordinary rice cultivars when influenced by N application rate.