Different interphases between the carbon nanotubes and the epoxy resin were constructed through the organic functionalization of carbon nanotubes. Effects of different functionalized carbon nanotubes on the glass transition temperature of the epoxy resin composites were investigated by using the dynamic mechanical analysis method; the roughness of epoxy resin composites was studied in the pendulum impact test. Results show that: the glass transition temperature of the composites with amination carbon nanotube is the highest, while that of the composites with carboxylation carbon nanotube is lower than that of the pure epoxy resin; toughness of the composites with embedded carbon nanotubes is doubled. These variation laws in the properties are attributed to the different interphases formed between the functionalized carbon nanotubes and epoxy resin matrixes.