Microwave irradiation at different frequencies gave molecular selective effects, namely higher frequency microwave effects for waters while lower frequency effects for ions. We already reported that 2.45GHz and 5.80GHz microwave irradiation gave different results for a hydrolysis reaction by thermostable β-Glucosidase HT1. Here, we designed and made a reactor, employed 400MHz microwave irradiation, and studied the effectiveness of 400MHz microwave for HT1 reaction, then 400MHz and 2.45GHz had the ability to accelerate HT1 reaction. In consideration of the general mechanism of enzymatic glycoside hydrolysis, our results would be reasonable if ions are key reaction species because 400MHz microwave activated ions selectively. In addition, the phenomenon that 400MHz microwave would not affect water molecules by dielectric heating might contribute the enzyme stability. This report should support that microwave is not only a tool to heat reactions efficiently but also can bring unique effects for reactions.