Cell autolysis could lead to a decrease in both cell viability and the production of biochemicals, presenting one of the significant challenges during fermentation. Bacillus licheniformis, a gram-positive bacterium widely used in the production of various biologic products, also confronts the limitation caused by cell autolysis. In this study, we investigated the impact of peptidoglycan hydrolases (LytC, LytD, LytE, CwlC), endopeptidase inhibitor IseA, and prophage gene xpf on cell growth and biochemical synthesis in B. licheniformis DW2. The results showed that the deletion of xpf and overexpression of iseA could significantly increase cell survival. Then, xpf was deleted on iseA overexpressed strain PP43UTR12iseA to construct engineered strain PP43UTR12iseAΔxpf, which further enhanced viable cells. The results of cell autolysis showed that PP43UTR12iseA could reduce cell autolysis significantly compared to the wild-type, but PP43UTR12iseAΔxpf did not further decrease cell autolysis. Furthermore, the production of bacitracin was 792.23 U/mL in the iseA overexpressed strain, which increased by 13.82% compared with the wild-type, but PP43UTR12iseAΔxpf did not further increase bacitracin production. Through detecting intracellular metabolites, we observed that iseA overexpression did not affect intracellular metabolism, but the precursors of bacitracin synthesis in PP43UTR12iseAΔxpf were lower than that of wild-type and PP43UTR12iseA. Finally, we found that the overexpression of iseA could also significantly improve the production of γ-PGA. In general, the overexpression of iseA could enhance the biomass and cell survival by reducing cell lysis without affecting the intracellular metabolites, which provided a potential strategy to improve production of biochemical.