Epoxy resin nanocomposites with different contents of multiwalled carbon nanotubes (MWNTs) are prepared. The interaction between MWNTs and the epoxy resin matrix and the microstructure and mechanical properties of the composites are systematically investigated by Fourier-transform infrared (FTIR) spectroscopy, transmission electron microscopy, scanning electron microscopy, and positron annihilation technology. FTIR spectra reveal that two kinds of hydrogen bonds exist at the interface for the nanocomposites modified by amine, one between the epoxy group on the side chain and the NH group, and the other between the epoxy group on the alicycle and the NH group. Compared to unmodified MWNT composites, the modified MWNT composites possess better mechanical properties, which are attributed to stronger interfacial interaction resulting from an efficient load transfer from matrix to MWNTs. Positron annihilation lifetime spectroscopy is used to characterize the microstructure of the epoxy/MWNT composites. The subtransition and glass transition temperatures are determined by finite-term positron lifetime analysis and the variation of the free-volume size as a function of temperature. Shifts of structure transition temperatures of the composites are observed with increasing MWNT weight content. Interestingly, the continuous lifetime analysis reveals the existence of two long-lived lifetime components above the glass transition temperature, which may be attributed to the formation of local ordered regions related to the packing density of chains.