Mono-dispersed nano-sized MCM-41 (M (with template)) particles were synthesized by sol-gel reaction. The effect of interface modification on the properties of epoxy composites was investigated. Modifications were carried out either by substituting silanol groups on the surface or in the mesopore channels into amine (M-NH2), calcinating mixture template in the mesopore channels (M(without template)), or recalcinating them at higher temperature to remove silanol groups (-OH) in the mesopore channels or on the surface (CM). Transmission electron micrograph results showed that the dispersing of MCM-41 nanoparticles was not influenced by the modification, while -NH2 group indeed modified the mesopore channels or the surface of MCM-41 particle by using IR, XRD, and N-2 adsorption-desorption. In addition, tensile tests suggested that M-NH2 nanoparticles could simultaneously provide epoxy matrix with strengthening and toughening effects. However, due to the different interfacial structures between the fillers and the matrix, the mechanical properties of the composites filled by M-NH2 were much better than those of composites filled by MCM-41 (without template), MCM-41 (with mixture template), and CM.