The microcapsule nanoparticles were prepared by in-situ copolymerization of hydrotalcites (MAH) with the polymer (MF, PF, PS and PU) monomers, respectively, where the MF-wrapped MAH (MAH@MF) had the best monodispersity. The composites of the microcapsules and EVA were prepared by incorporating the microcapsule nanoparticles into ethylene vinyl acetate (EVA), respectively. To further understand the intrinsic correlation between microcapsule fillers and EVA matrix, molecular dynamics (MD) simulation was introduced to qualitatively analyze the contribution of microcapsule fillers on improving compatibility and mechanical properties of the EVA matrix. The compatibility of microcapsule nanoparticles with EVA matrix were detected in sequence through SEM, DSC and tensile strength tests. And the combustion, thermal behavior and flame retardance were also characterized by TG analyses as well as LOI and UL-94 level. As a result, the MAH@MF filler had the best performances in improving the flame retardancy and mechanical properties among the microcapsule fillers, attributed to high compatibility of the MAH@MF and EVA matrix, which made uniform distribution of the MAH@MF filler due to the reciprocity of triazine functional ring with vinyl acetate linkages.