The currently available polyphenols delivery systems require the complicated preparation process and participation of multiple food-graded materials. Yeast membranes (YMS), as unitary encapsulation material, not only can load natural products by their porous structure but also can be specifically degraded by β-glucanase in intestine. Therefore, this study fabricated Malus baccata (Linn.) polyphenols loaded nanoparticles based on yeast membranes (YMS@MBP) by hydrogen bonding and hydrophobic interaction. YMS@MBP with the lamellar aggregated morphology possessed the non-crystalline feature and excellent thermal stability, and their average particle size was 997.2 ± 22.1 nm. Through establishing the model of gastrointestinal digestion in vitro, YMS@MBP presented the sustained release and intestinal targeting release characteristics, and the maximum release rates in gastric and small intestine were 16.04 % and 79.39 %, respectively. HPLC-MS/MS analysis showed that MBP were mainly composed by quercetin and its derivatives, phloretin, catechins, anthocyanins and phenolic acids. After digestion, the phenolic composition of MBP was perfectly protected by encapsulation of YMS, which was much closer to that of undigested MBP. This study provides a new strategy for construction of polyphenols delivery system applied in functional food field.