Crop quality tends to decrease with an increasing grain yield. Nitrogen is an important nutrient and moderate nitrogen foliage application (NFA) can significantly improve the wheat yield and quality. The objective of this study was to investigate the effect of NFA on the grain yield and quality of wheat and its genotype-dependent variation. Eighteen wheat cultivars were used, and two NFA levels (N1 and N2; 10.70 and 21.40 kg N ha−1 two day−1, respectively) were applied. Significant genotypic differences in the yield and quality were observed among the 18 varieties, and their responses to NFA differed. For nine varieties in the experiment, N1 increased the grain yield, but N2 did not. In contrast, high concentrations of NFA had no effect on the grain yield in the other nine varieties. The protein content and composition and trace element (Fe, Zn, etc.) are all nutrient elements that notably affect the wheat grain quality and yield. NFA significantly increased the grain prolamin and glutelin concentrations in the grains, thereby increasing the total protein concentration. The prolamin, glutelin, and total protein concentrations in the grains of the lower-protein cultivars were more sensitive to NFA than those of the higher-protein cultivars. In addition, NFA significantly decreased the amylose concentration in the grains. By affecting the prolamin, glutelin, and amylose concentrations in the grains, NFA significantly increased the development and stability times of the corresponding wheat flour dough, thereby improving the dough quality. Moreover, NFA reduced the molar ratio of phytic acid to Fe and Zn, increasing the bioavailability of trace elements. The judicious application of nitrogen fertilizer resulted in the synergistic improvement in the yield and quality.