The chemical composition of warm mix rubber modified asphalt with EM and SDYK were analyzed by Fourier transform infrared spectram(FTIR) and atomic force microscope(AFM), and index of each functional group was calculated. The adhesion, Derjaguin Muller Toropov modulus(DMT modulus) of nano scale mechanical properties of rubber modified asphalt were analyzed by preceding and post thermo oxidative aging. The results showed that after the addition of EM and SDYK, there is no obvious chemical change in asphalt, but the content of asphalt components is changed. Thermal oxidative aging leads to the reaction of oxidation and condensation, fracture and recombination among molecular in rubber modified asphalt, which changes the chemical composition and nano mechanical properties of asphalt. After thermal oxidative aging, rubber modified asphalt with warm mixing agent SDYK has the smallest increase in functional group index and in DMT modulus, and the smallest decrease in adhesion. The results show that its anti aging ability is better than that of asphalt with warm mixing agent EM and without warm mixing agent.