Abstract: Prebiotics with different degrees of polymerization could regulate the colloidal stability of fermented juice through distinct interfacial mechanisms. In this study, seedless red pitaya juice was used as a model system to investigate these mechanisms. After fermentation with a composite culture of lactic acid bacteria, 8% (w/w) fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), or inulin was individually incorporated into the fermented juice and homogenized. Unfermented juice and fermented juice without prebiotic supplementation served as dual controls. Physicochemical properties, flavor profiles, rheological behaviors, interfacial particle characteristics, multiscale microstructures, and thermal properties were systematically characterized. The results indicated that the three prebiotics enhanced colloidal stability through distinct chain-length-dependent interfacial mechanisms. FOS adsorbed onto particle surfaces to form hydrated steric barrier layers, thereby maintaining particle dispersion and stabilizing the mean particle size at 2.707 μm. GOS promoted particle flocculation through multipoint bridging interactions, increasing the consistency coefficient to 8.55 Pa·sⁿ. It also exhibited relatively high thermal stability, as indicated by an endothermic peak at 154.27 ℃. However, this was accompanied by an increase in the mean particle size to 6.614 μm. In contrast, inulin formed a three-dimensional network through long-chain molecular entanglement. This network reduced the centrifugal sedimentation rate to 17.90% and improved resistance to sedimentation. It also contributed to the retention of juice color. Fourier-transform infrared spectroscopy and X-ray diffraction analyses suggested that the interactions between prebiotics and the juice matrix were governed exclusively by non-covalent forces, primarily hydrogen bonding and molecular entanglement, without altering the chemical structure or crystalline characteristics of the system. Furthermore, FOS improved the sugar-to-acid ratio and achieved the highest sensory acceptability score (87.0). GOS exhibited superior rheological enhancement and thermal stability, making it particularly suitable for thermally processed products, whereas inulin showed distinct advantages in flavor retention and long-term storage stability. Overall, the findings highlighted the relationship between prebiotic chain length and the colloidal stability of fermented juice, providing mechanistic insights that may support the rational selection and application of prebiotics in functional fermented fruit and vegetable beverages.