Chronic wounds are highly susceptible to bacterial infections. Previously, we loaded a natural antimicrobial peptide of low cost and high safety, ε-polylysine (EPL), into the electrospun nanofiber mat of starch. The mat showed comparable antibacterial activity but markedly better biocompatibility than the commercial silver-containing dressing. To further optimize material property, in this paper, we use hyaluronic acid (HA) to replace starch. Results show that EPL-loaded HA nanofiber mats (OHA-EPL) have suitable water vapor permeability, good biocompatibility and broad-spectrum antibacterial property similar to that of EPL-loaded starch nanofiber mat (Starch-EPL). Differently, the content of EPL in OHA-EPL nanofiber mats increases from 19.2% to 27.9%, the tensile strength rises from 0.3 MPa to 0.6 MPa, the elongation grows from 62.0% to 130.0%, and the fiber degradation and EPL release accelerates. In addition, OHA-EPL can absorb up to 26.3-times exudate, which is much higher than Starch-EPL (15.1 times). Combined with the excellent biological activity of HA, OHA-EPL may produce better therapeutic effects than Starch-EPL.