The effects of MRS, whey protein and blueberry alone, and mixed fermentation on the survival rate of lactic acid bacteria under various freeze-drying conditions were investigated. The surface structure of the freeze-dried powders was also investigated to explore the anti-freezing protection mechanism of mixed whey protein and blueberry fermentation on the bacteria. It was found that the mixed fermentation medium of blueberry and whey protein has a protective effect on the freeze-drying bacteria and is better than the traditional MRS and whey protein medium. The optimal concentration of blueberry juice addition was 9%. The survival rate of the pre-freezing temperature at -80 °C was higher than at -20 °C after the pre-freezing and freeze-drying processes. The freeze-drying thickness of 0.3 cm could improve the survival rate of the bacteria. The Fourier transform infrared spectroscopy results indicated the interaction between the whey protein, anthocyanins, and the surface composition of the lactic acid bacteria.