[Objective] Based on the critical role of type I signal peptidase in the secretion system, this study explores the interaction between signal peptidase and signal peptides to guide the optimization of aminopeptidase secretion expression in Bacillus amyloliquefaciens. [Methods] The endogenous signal peptidase and signal peptide of Bacillus amyloliquefaciens TCCC 19030 were examined using relative fluorescence intensity and enzyme activity for analysis, and molecular docking to study their interaction. [Results] The signal peptide YolC fused with aminopeptidase exhibited the highest extracellular enzyme activity, reaching 11 847.67 U/mL. Overexpression of the signal peptidase SipW increased aminopeptidase activity to 16 261 U/mL. Molecular docking results also showed that YolC had the lowest binding free energy with SipW, at −4.4 kcal/mol. [Conclusion] Optimization of signal peptides and overexpression of signal peptidase can effectively enhance the secretion of aminopeptidase. The binding energy between signal peptidase and signal peptide is a key factor influencing the secretion levels of the target protein.