Soy protein isolate (SPI) and sodium carboxymethyl cellulose (CMC-Na) were combined in varying proportions and subjected to the Maillard reaction through spray drying and dry-heat methods. The effects of different mixing ratios and reaction times on the physicochemical properties of the reaction products were investigated, with a focus on their application as wall material for bifidobacterium lactis BB-12. The solubility of the system was significantly enhanced by the Maillard reaction, reaching its maximum at an SPI:CMC-Na ratio of 1:2. At this proportion, after a 6-hour dry-heat Maillard reaction, there was a significant increase in ultraviolet absorption and browning degree of the product, while the free amino acid content decreased significantly. Fluorescence spectroscopy revealed that the conformation around tryptophan residues remained in its natural form, whereas circular dichroism spectroscopy showed a decrease in α-helix and Random coil structure content upon addition of CMC-Na, accompanied by an increase in β-sheet and β-turn content. This stretching effect on protein molecules facilitated functional property expression. Compared to unencapsulated probiotics BB-12 microcapsules prepared using secondary spray drying with a wall-core volume ratio of 6:1 exhibited higher encapsulation efficiency along with good storage stability, tolerance to gastrointestinal conditions, and heat stability. These findings have practical implications for preserving bioactive substances in the food industry.