Low-temperature vacuum drying is one of the most important ways to product the probiotic powders. But different strains showed different freeze-drying resistance during the whole cycle. In order to find out what caused the different freeze-drying survival rate between Bifidobacterium animalis (B. animalis) CCFM1155 and Bifidobacterium adolescentis (B. adolescentis) CCFM8630. Focus on the differences on the strains’ own structure, the results showed B. animalis CCFM1155 had thicker cell wall than B. adolescentis CCFM8630. Cyclopropane fatty acid was reported to modulate the permeability and fluidity of the membrane, but the B. adolescentis CCFM8630 deficiency the cfa which controlled the synthesis of cyclopropane fatty acid caused lower freeze-drying survival rate of the strain. Generally, the B. adolescentis CCFM8630 accumulated more γ-aminobutyric acid (GABA) to overcome the acidic environment. However, after maintaining a constant culture pH, the content of the glutamate was increased in the B. adolescentis CCFM8630 and the freeze-drying survival rate of the strain was also increased. In summary, our research revealed that fatty acids and intracellular substance differences caused the different of freeze-drying survival resistance between B. animalis CCFM1155 and B. adolescentis CCFM8630.