The formation of Zein-chitosan complex coacervates (ZCSC) with a co-encapsulated bilayer structure were successfully fabricated from Zein (Z) and chitosan (CS) for co-encapsulating the curcumin (Cur) and quercetin (Que). A combination of electrostatic attraction, hydrophobic effects and hydrogen bonding was demonstrated to be responsible for the formation of bilayer structure with chitosan covering on the surfaces of the Zein nanoparticles co-loading with curcumin and quercetin. The impacts of pH, type of polyphenols, protein-polyphenol ratio and curcumin-quercetin ratio on formation mechanism of bilayer structure was studied using the size, PDI, ζ-potential, size distribution and phase diagram measurement. The chemical structure and microstructure were further explored by Fourier transformed infrared spectroscopy (FTIR), UV–visible spectroscopy and Scanning electron microscope (SEM). Interestingly, the phase diagram and SEM images revealed that larger coacervates were favorably formed far away from the polyphenol-polyphenol ratio of 1:1 and near neutral pH. The bilayer-structured complexes showed high encapsulation efficiency (EE) for curcumin and quercetin, as well as a slow-release effect for both compounds. Additionally, these complexes were physically stable throughout a 3-week storage period. In conclusion, the nano-scale complexes and micron-level coacervates with a co-encapsulated bilayer structure based on hydrophobic Zein core and hydrophilic chitosan shell are an effective co-delivery system for two bioactive agents with different molecular characteristics.