Bifidobacterium bifidum BB01 was microencapsulated by extrusion method with sodium alginate. This paper aimed to study the survival rate of microencapsulating Bifidobacterium bifidum BB01 in simulated gastrointestinal conditions, resistance to artificial bile salt and stability during storage. Results showed non-microencapsulated Bifidobacterium bifidum BB01 were more susceptible than microencapsulated under simulated gastrointestinal conditions, and microencapsulated Bifidobacterium bifidum BB01 exhibited a lower population reduction than free cells during exposure to simulated gastrointestinal, The enteric test showed that the microorganism cells were released from the monolayer microcapsules, double microcapsules and trilayer completely in 40min. The viable counts of monolayer microcapsules, double layer microcapsules and triple layer microcapsules decreased by nine magnitudes, four magnitude and one magnitude after 2h, respectively. Moreover, in fruit orange, pure milk and nutrition Express, the optimum storage times of free Bifidobacterium bifidum BB01, monolayer microcapsules, double layer microcapsules and triple layer microcapsules were 21 days, 21 days, 28 days and more than 35 days at 4°C, but at room temperature the optimum storage time were 7 days, 14 days, 21 days and more than 28 days, and the viable counts were maintained at 1×106 CFU g−1 or more.