Two hundred and ninety F9 recombinant inbred lines (RILs) derived from the bread wheat cultivar Gaocheng 8901 and the waxy wheat cultivar Nuomai 1 were used in determining the high-molecular-weight glutenin subunit (HMW-GS) and waxy protein subunit combinations and their effects on the dough quality and texture profile analysis (TPA) of cooked Chinese noodles. Seven alleles were detected at Glu-1 loci. There were two alleles found at each of the Wx-A1, Wx-B1 and Wx-D1 loci. Eight allelic combinations were observed for HMW-GS, LMW-GS and waxy proteins, respectively. Both the 1/7+8/5+10 and 1/7+8/5+12 combinations contributed to dough elasticity, and the 1/7+8/5+10 combination also provided better TPA characteristics. Compared to Wx protein, HMW-GS was more important on dough alveogram properties. LMW-GS significantly affected springiness and cohesiveness; HMW-GS mainly affected the hardness; Wx×LMW-GS significantly affected the springiness, cohesiveness and chewiness; HMW-GS×Wx×LMW-GS mainly influenced the springiness and chewiness. But HMW-GS×LMW-GS only affected the spinginess. These indicated the TPA of noodles was significantly affected by the interactions between glutenin and Wx proteins.