Abstract: To improve the stability and bio-accessibility of quercetin and increase the added value of jujube peel, this paper continued the extraction of pectin from the residue of extracted jujube peel pigment. Then, quercetin was encapsulated using jujube peel pectin and cellulose nanocrystals (CNC) as the wall material to construct quercetin microcapsule system, and the preparation process was optimized through single-factor experiments and response surface tests. The microcapsules were characterized using environmental scanning electron microscopy (ESEM), Fourier transform infrared spectroscopy (FT-IR), and thermogravimetric analysis (TGA), and their storage stability and in vitro simulated digestion properties were investigated. The results showed that the pectin extraction yield from the pigment residue was about 11 times higher than that from the jujube peel, and the optimized quercetin microcapsule embedding rate was increased to 74.73%±2.45% which was an improvement of over 15%. The ESEM revealed that the microcapsules were amorphous powder with a wrinkled surface and visible dents. The particle size was 2.625±1.124 μm, with a PDI of 0.286±0.163, and their moisture content was 2.97%±0.40%. FT-IR and TGA analyses confirmed the successful encapsulation of quercetin by the composite wall material. Quercetin retention in the microcapsules was about 20% higher than that of free quercetin after two weeks of storage at 4 ℃ and 37 ℃, and the bio-accessibility of quercetin after encapsulation was 2.5 times that of free quercetin. Effective encapsulation and controlled release of quercetin with enhanced stability and improved bio-accessibility were achieved. This study provides a theoretical basis for the development of quercetin-related products and the comprehensive utilization of jujube peel, a by-product of jujube processing.