Cell microencapsulation is a promising approach for cell implantation, cell‐based gene therapy, and large‐scale cell culture. The well‐studied α‐AP (alginate–α‐poly‐L‐lysine) microcapsules have been restricted to large‐scale cell‐culture and clinical applications because of high costs and cytotoxic effects in some cases. This study used ϵ‐poly‐L‐lysine (ϵ‐PLL), a high‐biocompatible and low‐cost food additives produced by fermentation, to prepare ϵ‐AP (alginate–ϵ‐PLL) microcapsules with various thickness membranes and swelling behaviors. ϵ‐AP microcapsules were permeable to BSA, a standard protein of culture medium. ϵ‐AP‐microencapsulated Chinese hamster ovary (CHO) cells proliferated with culture time; no obvious difference with α‐AP‐microencapsulated CHO cells during the early 19 days. Whereas ϵ‐AP‐microencapsulated CHO cells kept higher viability (OD = 0.646 ± 0.012) on the 22nd day and microcapsule strength (integrity rate of 88%) on the 24th day than that of α‐AP microcapsules (OD = 0.558 ± 0.025, integrity rate of 80%). ϵ‐AP (alginate‐ϵ‐PLL) microcapsules exhibited more superior properties and could lower the costs to broaden the applications of microencapsulation technology. © 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2013.