High-molecular-weight glutenin subunits (HMW-GSs) are important components of gluten, which determine the grain quality of wheat. In this study, we investigated the effects of nitrogen (N) fertilizer application on the synthesis and accumulation of grain protein and gluten quality in wheat lines with different HMW-GSs absent. The results showed that the absence of the HMW-GS in the wheat variety Ningmai 9 significantly decreased the contents of gluten, glutenin macropolymer (GMP), protein compositions, HMW-GS and HMW-GS/LMW-GS. The reduction in glutenins was compensated to some extent by an increase of gliadins. The absence of x-type HMW-GSs (1, 7 and 2 subunits) had a greater effect on gluten and GMP properties than y-type HMW-GSs (8 and 12 subunits). The content of protein compositions, gluten and GMP increased with an increase of N level; however, the increment in wheat lines with the absence of HMW-GS, especially in Ax1a, Bx7a and Dx2a, was lower than that in the wild type under various N levels. The expression level of genes encoding HMW-GSs, and activities of nitrate reductase (NR) and glutamine synthetase (GS), differed significantly among the investigated wheat lines. The reduction in gene expression and activities in Ax1a and Dx2a may account for the reductions in gluten, GMP, protein compositions, HMW-GS and HMW-GS/LMW-GS.