The effect of low energy ultrasound in biochemistry and biotechnology has attracted great attention in recent years. It can enhance substrate dissolution and improve mass transfer within and outside of a cell, both of which are beneficial to the synthesis of fructose ester. Here we describe the experimental study of the effect of ultrasounds of different intensity on the lipase-catalyzed synthesis of fructose ester in the solvent butanone. The results were compared with control reactions performed with no ultrasound. High performance liquid chromatography (HPLC) and thin layer chromatography (TLC) were used for qualitative and quantitative analyses. The results show the following: 1) the concentration of mono-ester and diester increased with the reaction time, either with or without ultrasonic irradiation. Low energy ultrasound accelerated the reaction due to the effect of ultrasonic steady cavitations, and high energy ultrasound was not beneficial to the reaction. 2) The application of ultrasound played an important role in our lipase-catalyzed reaction. It decreased reaction time as compared to a reaction without ultrasound that resulted in the same yield, increased reaction rate, and enhanced the amount of fructose ester produced. When the frequency was 10 kHz and sound intensity was 0.16 W·m, the concentration of ester was twofold more than without ultrasonic irradiation after a reaction time of up to 12 h. With the proper ultrasonic parameters, the overall concentration of production appeared to increase exponentially with the reaction time. 3) Ultrasound had little effect on the initial reaction rate, and continuous ultrasonic irradiation was favorable for the reaction. The longer the reaction continued, the more obvious the effects of the ultrasound became in our experiments.