Wheat (Triticum aestivum L.) quality is a major focus of wheat breeding that is influenced by multiple factors. The Huang-Huai wheat region is one of the main wheat-producing areas in China, and it has favorable conditions for cultivating wheat cultivars with strong-gluten and medium-strong-gluten. In this study, a systematic assessment of seven crucial quality traits and two important genetic loci (Glu-1 and Sec-1) in 436 wheat cultivars in the Huang-Huai wheat region of China by principal component analysis (PCA) and fuzzy comprehensive evaluation (FCE) methods identified the stability time (ST), stretch area (SA), and maximum resistance (MAXR) as three key factors which significantly influence wheat quality. Glu-1and Sec-1 primarily impacted these three traits and subsequently influenced wheat quality. Compared to Glu-A1 and Glu-B1, Glu-D1 has a more significant impact on the comprehensive evaluation value D, principal components PC1–PC3, and the main traits ST, SA and MAXR of PC1. Wheat cultivars carrying the high-molecular-weight glutenin subunit (HMW-GS) Dx5+Dy10 exhibited notable improvements in the ST, SA, and MAXR traits compared with those carrying HMW-GS Dx2+Dy12, suggesting that Dx5+Dy10 may enhance wheat quality by improving those traits. By combining the results of the D value, genotype by yield×trait (GYT) index, and HMW-GS score, 20 high-quality and high yielding wheat cultivars were identified, which can be used as elite parents for wheat quality breeding.