This study aimed to explore the feasibility of using a complex coacervation reaction of Zein and chitosan (CS) to construct bilayer microencapsulation with both hydrophobic inner core and hydrophilic outer shell as a carrier for dual-functional factors delivery, and further investigate the protective effect of this co-delivery microencapsulation on probiotics. It was demonstrated by the study that the binding of Zein and chitosan was dependent on their pH. As the pH increased, the electrostatic interactions were strengthened, leading to the formation of larger particles with a weak positive charge (ζ = 7.37 mV) (d = 2.75 μm) that could weakly electrostatically adsorb Lactobacillus casei (ζ = −0.96 mV). SEM images showed that they gradually assembled from single-layer complexes into bilayer structured Zein-chitosan complex coacervates (ZCSC). FTIR analysis confirmed the presence of hydrogen bonding in ZCSC. Specifically, compared to no polyphenols, lower polyphenols content (quercetin, 0.05%) was found to improve probiotic activity (over 6.23 × 109 cfu/mL) and encapsulation efficiency (over 19.3%), confirming the superiority of polyphenols in hybrid co-encapsulation microcapsules. In addition, during simulated gastric digestion, being encapsulated in ZCSC increased probiotic survival by 62.85% compared to free probiotics. Polyphenol-containing ZCSC further enhanced probiotic growth during storage. Finally, using the ZCSC as a fermenting agent, a new type of flavored fermented milk with multiple functions was prepared. In conclusion, this study emphasized the potential of using layered microcapsules to deliver and protect probiotics and polyphenols, providing valuable inspiration for developing new functional foods with higher bioavailability and therapeutic effects.