A multilayer composite micro-particle structure from the inside thereof includes a core body and an exterior structure body in order. The core body includes natural extracts, probiotics, or the combination thereof. The exterior structure body from the inside thereof includes an encapsulation body and a protective layer in order. The encapsulation body encapsulates the core body. The protective layer has a membrane-shaped structure, encapsulating the encapsulation body, which prevents the inactivation of the ingredients of the core body from the gastric acid in human digest tract so as to increase the storage stability of the ingredients of the core body and the absorption of the body.一種含活性成分之多層複合微粒結構,由內而外依序包括核心體及外層結構體。核心體,包含天然萃取物、益生菌或其組合。外層結構體由內而外係依序包含包覆體及保護層。包覆體係包覆於核心體外,保護層係為膜狀構造,包覆於包覆體外,防止核心體成分受到人體腸胃道中的胃酸破壞,藉此提高核心體成分的安定性及人體吸收率。