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The regulation of flocs derived from polyphenol–protein formation in milk tea has not been fully explored. In this study, the flocculation of milk tea was regulated by adding 10 kinds of stabilizers with different characteristics. The stability coefficient and centrifugal precipitation rate were used as indexes. The optimal concentration ratio of the complex stabilizer was identified using the response surface methodology (RSM), being 0.04% for Arabic gum, 0.02% for β-cyclodextrin and 0.03% for Agar. Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to analyze the characteristics of different stabilizers in milk tea, and our findings were as follows: (1) The relative strength of the peaks in different stable systems was different. The absorption peaks were mainly near the wave numbers 3376 cm−1, 2928 cm−1, 1655 cm−1, 1542 cm−1, 1408 cm−1, 1047 cm−1 and 925 cm−1. (2) The milk tea system was an amorphous structure. The diffraction peak of the composite system was observed to be about 20°. The crystallinity of the milk tea in the compound group was 33.16%, which was higher than that of the blank group (9.67%). (3) The compound stabilizer reduced flocculation, and the stabilizing agents improved the surface order of milk tea. These results indicate that the combination of polysaccharide stabilizers (Arabic gum and agar) and oligosaccharide stabilizers (β-CD) in certain proportions can regulate the flocculation of milk tea and improve its stability. The potential research avenues involving polyphenol–protein complex instability systems and their applications in food development are expanded by this work.