A robust heterogeneous Mn catalyst for selective epoxidation was prepared by the attachment of a Mn4 oxonuclear complex [Mn4O2(CH3COO)7(bipy)2](ClO4)·3H2O (1) on SiO2 and the successive stacking of SiO2-matrix overlayers around a supported Mn cluster. The structures of supported Mn catalysts were characterized by means of FT-IR spectroscopy, diffuse-reflectance UV/vis spectroscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, and Mn K-edge X-ray absorption fine structure. A ligand exchange reaction between the CH3COO ligand of 1 and surface silanol group produced a SiO2-supported Mn cluster (2), whose coordination structure was similar to 1. Subsequent heating of 2 under vacuum yielded supported Mn clusters (3, 4) through the partial elimination of CH3COO ligands. The surface-attached Mn clusters of 2, 3, and 4 were easily released to a reaction solution under epoxidation conditions (Mn leaching: approximately 50%), although they were active for epoxidation of trans-stilbene (the conversion of trans-stilbene, 99%, and the selectivity of trans-stilbene epoxid, 96%, for 6 h on 3). We found that the functionalization of the supported Mn cluster on 2 with surface SiO2-matrix overlayers altered the reactivity of the supported Mn cluster. Dimeric Mn species (5c) with reduced Mn oxidation state and coordination numbers was formed together with a reaction nanospace surrounded by the SiO2-matrix overlayers. By optimizing the stacking manner of the SiO2-matrix overlayers, the durability of the Mn catalyst was remarkably improved from leaching (the Mn leaching reached the minimum value of 0.01%), and active and stable epoxidation performances were successfully achieved in the heterogeneous phase (the conversion of trans-stilbene, 97%, and the selectivity of trans-stilbene epoxide, 91%, for 31 h on 5c).