A mathematical model of microwave drying kinetics based on Fick's second diffusion law was established and and the influence of microwave drying on ferulic acid (FA) and hydrosafflower yellow A (HSYA) in Shuxiong prescription was studied. The proposed model has been verified by using experimental data from microwave drying of Shuxiong prescription. By increasing the microwave output power (500-650 W) and the sample amount (15-60 g), the diversion rate of FA and HSYA changed. In order to determine the kinetic parameters, the drying data were fifed to various models based on the ratios of differences between the initial and final moisture contents and equilibrium moisture content versus drying time. The activation energy was calculated using an exponential expression based on Arrhenius equation. The relationship between the drying rate constant and effective moisture diffusivity was also estimated, and it showed linear.