Lactobacillus rhamnosus GG (LGG) microcapsules prepared using the complex coacervation method were dried through spray and vacuum freeze drying. Physical properties, resistance to simulated gastrointestinal and bile salt conditions, and the stability of the LGG microcapsules during storage and heat treatment were estimated. Spray and vacuum freeze drying are suitable for LGG microcapsule preparation because of lower than 2.80% of the water content, and higher than 93.21% of the encapsulation efficiency. Under the simulated gastrointestinal condition, the survival rates of two kinds of microencapsulated LGG were over 96%. At 0.6% bile salt concentration, the survival rate of microencapsulated LGG subjected to spray drying was 110.89% higher than that of LGG subjected to vacuum freeze drying. In addition, the stability of the former was better than that of the latter during storage under low water activity condition (0.11). However, under high water activity condition (0.75), the two showed opposite results. The two kinds of microencapsulated LGG were completely inactivated after 4 weeks in 0.75 of water activity. The survival counts of microencapsulated LGG had no significant difference at −18 • C after 8 weeks. After 8 weeks at 25 • C and 4 • C, the survival loss of microencapsulated LGG through drying and vacuum freeze drying was approximately 2 and 1 log CFU/g, respectively.