The interest in anthocyanins used in food, cosmetic, and pharmaceutical industries has increased the research in order to improve their stability while maintaining bioactivity. In this work, cyanidin-3-glucoside lauryl ester (Cy3glc-C12) was enzymatically synthesized, using Novozym 435 as a catalyst, as well as to obtain a kinetic model for the bioprocess. Its liposolubility, UV–VIS absorbance property, thermostability, and potential proliferative effect on intestinal probiotics were also studied. The maximum conversion yield (68.7 ± 2.1%) was obtained with a molar ratio (substrate:donor) of 1:56, 435 16.5 g/L Novozym, temperature of 56 °C, and a time of 28 h via the acylation occurred at 6²-OH position of the glucoside. The kinetics of the reaction is consistent with a ping-pong bi-bi mechanism and the parameters of the respective kinetic equations are reported. Compared with native Cy3glc, the liposolubility, pH resistivity and thermostability of Cy3glc-C12 were significantly improved. The growth kinetics of Bifidobacteria and Lactobacillus was established based on the Logistic equation, and Cy3glc-C12 could promote their proliferation especially during the logarithmic growth, in which lower pH and more bacteria population were found compared with those of media without anthocyanins. This research provided a reference for the industrial production of Cy3glc-C12 and extended its application to natural products in lipophilic systems.