Phospholipid-based nanovesicles (PBN) are effective in drug delivery and bitterness masking, but they often lack stability, and traditional emulsion microcapsules fail to mask flavors effectively. This study aimed to develop a phospholipid-based nanovesicle microcapsule (PBN-M) with a dual vesicle-shell structure to encapsulate (-)-epigallocatechin-3-gallate (EGCG), enhancing its stability and bitterness masking. PBN-M was created using an emulsion transfer template method and spray drying. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed a 200 nm PBN core with a 40 μm shell. In vitro studies showed that the vesicle-shell structure efficiently released EGCG and minimized degradation in the intestines. Storage tests indicated that interactions between whey protein isolate and gum arabic formed a thicker shell, improving EGCG stability. Sensory evaluations confirmed significant bitterness masking. These results suggest that PBN-M is promising for stable, flavor-masked EGCG delivery, enhancing the functional and sensory qualities of bioactive ingredients.