In order to change the binding polyphenols into free polyphenols in apple juice, improve the content of functional polyphenols, and develop products of apple juice with health care function, Lactobacillus acidophilus 6005, Lactobacillus plants 21805 and Lactobacillus fermentum 21828 were mixed and fermented with apple juice, which was mixed with three varieties of Aksu, Qinguan and Granny Smith. The changes of viable cell numbers and physicochemical composition in apple juice fermentation process were studied. In addition, the kinetic model of bacterial growth and the kinetic model of total phenolic acid incremental change were established and verified. The results showed that probiotics grew well in apple juice, and the number of viable bacteria exceeded 2.68×108CFU/mL. During fermentation, the total sugar content was decreased, the titratable acid content was increased, and the total phenolic acid content was increased. Moreover, the content of several functional phenolic polyphenol was increased, such as chlorogenic acid and gallic acid. Probiotic fermentation changed the quality of apple juice. The kinetic model of bacterial growth and the kinetic model of total phenolic acid change were established. The average error between the theoretical and experimental values of the model was less than 10%. The fitting was good and the established kinetic model could predict the fermentation process. The research results provided a theoretical basis for the development of functional juice beverage products.