Short branched-chain fatty acids (SBCFAs) are multi-functional platform chemicals used in many fields. Currently, SBCFAs are produced mainly by chemical synthesis, which is high cost and lead to environmental pollution. The aim of this study was to achieve high-level production of SBCFAs from waste materials, bean dreg and crude glycerol. The Bacillus licheniformis DWc9n* was genetically modified by overexpression of SBCFAs synthesis genes via replacement of native promoter of bkd operon, the mutant strain DWc9n*-PbacA produced 4.68 g/L of SBCFAs, increasing by 1.98-fold compared to wild-type strain. SBCFAs concentration was further increased to 7.85 g/L through process optimization. In a 5-L batch fermenter, the mutant showed SBCFAs production with high concentration (8.37 g/L) and productivity (0.20 g/L/h), which is the highest level of SBCFAs production based on low-value substrates fermentation. This is the first study describing efficient SBCFAs production by the modified B. licheniformis strain from bean dreg and crude glycerol.