Human β-defensin 3 (DEFB103) is a recently identified small cysteine-rich cationic peptide expressed ubiquitously upon local microbial invasion. A number of accumulating evidences indicate that this peptide is involved in many biological processes, including microbicidal activities, chemoattraction, and immunomodulation. In this article, we describe a novel approach through which we performed the expression and purification of the recombinant DEFB103 peptide in Escherichia coli (E. coli) based on the pTWIN1 expression system. This approach does not introduce any extra residues to the peptide product, and also eliminates the requirement of removing the fusion tag by exogenous proteases. A high yield of 112 mg of soluble fusion DEFB103 was obtained in 1 liter of Luria-Bertani (LB) medium. By one-step affinity chromatography and on-column, auto-cleavage of the fusion tag, the mature DEFB103 peptide was produced with a yield of 30 mg/L LB. The purified DEFB103 peptide demonstrated strong antimicrobial activities against E. coli, S. aureus and C. albicans, which were representatives of Gram-negative and Gram-positive bacteria and fungi, respectively. Using this novel approach, we have successfully expressed and purified several human defensins with significant bioactivities. Our work may be helpful for structural and functional studies of other human defensins, and also for the production of human defensins.