ε-polylysine (ε-PL) is a polypeptide that shows broad-spectrum inhibition against both Gram-positive and Gram-negative bacteria, and it’s mainly produced by Streptomyces sp. However, the biosynthesis mechanism of ε-PL by Streptomyces sp. is still unclear. Herein, the metabolomic analysis of the biosynthesis mechanism of ε-PL in the original strain TUST and the high-yield mutant strain 6#-7 were investigated. Results show that the difference on metabolisms between TUST and 6#-7 was significant during fermentation periods. And based on further analyses of the results of both metabolomics and enzymatic activity, a possible metabolic regulation mechanism of the high-yield mutagenized strain 6#-7 was proposed. The transport and absorption capacity for glucose of strain 6#-7 is improved. And the activity of enzymes relating to ε-PL synthesis, including Hexokinase (HK) et al., is strengthened. On the contrary, the activity of enzymes in the branched-chain pathways, such as Succinate dehydrogenase (SDH) et al. is decreased. Meanwhile, the increase of trehalose, glutamic acid and proline makes the strain 6#-7 more resistant to ε-PL. Moreover, the strain 6#-7 has stronger ability to transfer ε-PL out the cell. Thus the ability of the mutagenized strain to synthesize ε-PL is enhanced and the strain 6#-7 can produce more ε-PL compared with the original strain. These findings provide a theoretical basis for further improving the production of ε-PL.