The preparation of oligochitosan with excellent performance via in situ enzymatic hydrolysis of chitosan by amylase in ionic liquid system is reported. It has been found that [Gly]BF4 ionic liquid leads to the good solubility and assistant degradation for chitosan, as well as good biocompatibility for amylase. In the homogeneous system that contained 1.0 g chitosan (degree of deacetylation = 88.5%) and 99.0 g 2 wt % [Gly]BF4 aqueous solution, oligochitosan with 2200 viscosity-average molecular weight has been obtained after 0.12 g amylase being used for 3 h at 50°C and pH 5.0. This result is superior to that conducted in acetic acid system. Moreover, [Gly]BF4 can be easily separated from the product and reused with only slight performance loss (oligochitosan product with 2700 viscosity-average molecular weight has been obtained after [Gly]BF4 being reused for five times). In addition, the mechanism for enzymatic hydrolysis of chitosan in [Gly]BF4 ionic liquid has been described. The research on the moisture-absorption, -retention, and antibacterial activity of oligochitosan product shows that the smaller molecular weight would bring the better moisture-absorption and antibacterial properties. The oligochitosan product with 2200 viscosity-average molecular weight exhibits preferable antibacterial properties to S. aureus and E. coli. At the same time, the moisture-absorption and -retention capacity of the above product can reach 32% (relative humidity (RH) = 43%), 62% (RH = 81%), and 150% (RH = 43%), 35% (dry silica gel) respectively. The enzymatic preparation of oligochitosan through [Gly]BF4 ionic liquid/water homogeneous system can be an efficient and environment-friendly method for academics and industry. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 41152.