Natural Monascus yellow pigments (MYPs) have received considerable attention due to their great safety and biological activities, but their unsatisfactory color tonality and stability limit their applications. A novel encapsulate system for hydrophilic yellow pigments (HYPs) were investigated through stable ternary nanocomplexes using quercetin-Sn (II), bovine serum albumin (BSA), and chitosan (CS) in this work. Layer-by-layer assembly preparation of HYPs-loaded quercetin-Sn (II)-BSA-CS nanocomplexes were verified by fluorescence spectroscopy, fourier transform infrared spectroscopy, X-ray photoelectron spectra, and 1H nuclear magnetic resonance. A hyperchromic effect on HYPs was obtained since their maximum ultraviolet absorption wavelength redshifted from 352 nm to 364 nm first due to the interaction with quercetin-Sn (II) and further redshifted to 408 nm due to ternary conjugation, greatly improved the color tonality and dye-uptake. The HYPs-loaded nanocomplexes showed irregular glomerate nanosphere with 252–382 nm of particle size. Their conjugation remitted HYPs degradation under various environmental stresses (thermal, light, and ascorbic acid treatment), and had a great color stability response to pH change. Higher lipid-lowering and antioxidant activities were detected in the nanocomplexes than free HYPs. This study provides a new way for fabricating novel MYPs with great physicochemical stability, bright color and hypolipidemic activities.