This study investigated the effects of different wheat flour extraction rate (35–95%) on the protein digestibility of those noodles. And to further elucidate the internal mechanism of above phenomenon, wheat flour with different amounts of wheat bran dietary fiber (WBDF) was produced by adding endogenous WBDF. Results indicated that protein digestibility rose significantly with increasing flour extraction rate, peaking at 91.85% at 80% extraction, before trending downward to 85.71% at 95% extraction. Further, among noodles containing different WBDF content, increasing WBDF content to 6% enhanced the formation of β-sheets, boosting I755 levels and reducing I854/I830 levels, thus decreasing protein digestibility. As WBDF content rose further, it promoted transition from β-sheets to β-turn, decreasing I755 and increasing I854/I830, enhancing protein digestibility slightly. The changes indicated that low level of WBDF induced a more compact protein secondary structure to inhibit protein digestion. Conversely, in noodles with high level of WBDF (>6%), the looser protein secondary structure partially alleviated the inhibitory effect of WBDF on protein digestion, which was caused by part of WBDF penetrating the protein's hydrophobic core. Moreover, the static quenching effect of WBDF on pepsin hydrolysis sites through hydrophobic interaction, especially the tyrosine, was another significant factor inhibiting protein digestion.