To further enhance the secretory expression level of xylanase (Xylanase, XynB), the locus of endogenous highexpression glucoamylase (Glucoamylase, GlaA) of Aspergillus niger was used as the target site for gene integration. Based on the six-copy strong promoter of the glaA gene, the expression and secretion of xynB were regulated by the signal peptide SglaA from glucoamylase and the signal peptide SpepB from acid protease B (Acid Protease B, PepB), respectively. Additionally, the impact of deleting the high-background protein acid-stable alpha-amylase (Acid-stable alpha-amylase, AsAA) on XynB secretion was also investigated. The results indicated that the recombinant strains TgX, TpX, ΔAgX, and ΔApX all displayed significant XynB protein bands at approximately 22 kDa. Among them, the xylanase activity of strain ΔApX (21 413.74 U/mL) was elevated by 70.67%, 14.92%, and 35.42% compared with the strains TgX, TpX, and ΔAgX, respectively. The signal peptide exerted insignificant effects on the transcription levels of the xynB gene and UPR marker genes. The deletion of high-background protein AsAA could enhance the transcription level of the xynB gene and facilitateds the folding and secretion of the recombinant protein, thereby alleviating endoplasmic reticulum stress. In summary, this study successfully optimized and enhanced the expression of XynB in Aspergillus niger based on efficient secretion of signal peptides and the deletion of high-background proteins, which lays a foundation for further research on improvement of XynB.