In this study, sodium alginate and chitosan were used together to embed Streptococcus thermophilus in the presence of galactooligosaccharide (GOS) for the preparation of alginate/chitosan bilayer synbiotic microcapsules. The preparation process and the storage stability and controlled release of the resulting microcapsules were investigated. The bilayer synbiotic microcapsules prepared at a sodium alginate concentration of 2 g/100 mL had desired appearance, particle size and embedding rate and were found to be stable when exposed to simulated gastric fluid; however, complete disintegration of these microcapsules and consequent complete release of Streptococcus thermophilus were observed when the exposure time was up to 150 min. The survival rate of free Streptococcus thermophilus in suspensions with or without added GOS declined greatly after refrigerated storage, only 0.32% on the 13th day for Streptococcus thermophilus suspension in the absence of GOS compared to 14.64% for the presence of GOS. For bilayer synbiotic microcapsules, the bacterial survival rate descended only slightly during the entire storage period regardless of the presence or absence of GOS and remained as high as 93.64% and 87.98%, respectively.