In this study, the efficient production of alkaline serine protease from engineered Bacillus amyloliquefaciens was achieved using feather meal as nitrogen sources. By screening of signal peptides library, a recombinant strain HZ12/SP2 with alkaline protease activity of 399.00 U/mL was constructed, which was 357% higher than the control strain HZ12/SP0. Furthermore, the alkaline protease activity was increased by 47%, up to 586.73 U/mL by deletion of the genes pssA, clsA, and sigF. Finally, the feather meal was used as nitrogen sources, and the strain ΔFCP/SP2 produced a maximum protease activity of 688.42 U/mL, which was 580% higher than the strain HZ12/SP0. In conclusion, an efficient alkaline serine protease-expression strain was constructed, which realized the valuable reuse of feather waste as nitrogen sources.