The core of the composite nanoparticles is constituted by quercetin (Que) and zein (Zein), while sodium caseinate (SC) or SC-sodium alginate (SA) serves as the shell. The nanoparticles are stabilized by a single layer of SC, which is embedded in a zein matrix. Double-shell-layer-stabilised Zein nanoparticles were prepared by antisolvent precipitation and electrostatic adsorption methods, with Que (Q-Z-SC) and SC-SA. These nanoparticles were embedded in the Que-Zein-SC-SA composite nanoparticles (Q-Z-SC-SA). The effects of m(Que)∶m(Zein) and m(SC)∶m(SA) on the particle size distribution and zeta potential of Q-Z-SC, Q-Z-SC-SA, and the embedding of Que were investigated under the condition of m(Zein)∶m(SC) based on the nanoparticle size and zeta potential analysis as well as the Que embedding rate test. The interaction mechanism of Q-Z-SC and Q-Z-SC-SA formation was explored by FTIR characterisation, and the effects of pH and ionic strength (NaCl solution concentration) on the stability of Q-Z-SC, Q-Z-SC-SA and Que release under simulated gastrointestinal conditions were analysed by stability and in vitro simulated release experiments. The results demonstrated that the average particle size of Q-Z-SC (Q1-Z25-SC25), prepared by a molar ratio of Que:Zein of 1∶25, was 158.2 nm, with a Que encapsulation rate of 79.53%. Q-Z-SC-SA, prepared by a molar ratio of Que∶Zein of 1∶25 and SC∶SA of 25∶7.5, exhibited an average particle size of 251.6 nm and a Que encapsulation rate of 90.71%. m(Que)∶m(Zein) = 1∶25 and m(SC)∶m(SA) = 25∶7.5 (Q1- Z25-SC25-SA7.5) with an average particle size of 251.6 nm demonstrated a significant increase in the encapsulation of Que, reaching 90.71%. The formation of the composite nanoparticles was driven by electrostatic, hydrogen bonding and hydrophobic interactions. Both Q1-Z25-SC25 and Q1-Z25-SC25-SA7.5 exhibited excellent pH and ionic strength stabilities, as well as the capacity to regulate the release of Que under simulated gastrointestinal conditions. The gastrointestinal conditions were simulated using the following parameters: gastric digestion stage (87.23% Que release rate) and enteric digestion stage (69.4% Que release rate). The Que release rates were 11.04% and 22.64%, respectively.