Selectively epoxidized trans-1,4-polyisoprene (SETPI) and randomly epoxidized trans-1,4-polyisoprene (RETPI) were fabricated successfully through modified surface water-phase suspension epoxidation and solution random epoxidation, respectively. The effects of fabricated method and epoxy degree of ETPI on the glass transition temperature (T (g)), dynamic mechanical properties and phase separation phenomenon of the as-fabricated polymer have been investigated by different scanning calorimetry, dynamic mechanical analyzer and phase contrast microscope. The double bonds and epoxy groups sequence structure distribution of different ETPI have been observed and analyzed by C-13-NMR. There is a great deal of difference in the microstructure and sequence distribution of epoxy group in ETPI with different synthesis methods and epoxy degree. The results show that distribution of epoxy group in SETPI is nonuniform which brings about the phase separation.