The phase structure of polypropylene thermoplastic elastomer (PTPE) is always a multiphase system in the preparation process. Under the condition of limited compatibility between polypropylene (PP) and elastomer, it is difficult to control the dispersion uniformity, size and morphology of each component domain between PP and elastomer. In order to make PTPE have homogeneous domains, easily controlled morphology and structure, and stable mechanical properties, microphase separation PP thermoplastic elastomer (MS-PTPE) was prepared based on the homogeneous system of PP and elastomer, and the chemical structure of MS-PTPE was studied by fractional extraction method. The results show that MS-PTPE is composed of unreacted PP, unreacted elastomer, graft copolymer of PP and (or) elastomer with bridging agent chain, and crosslink between elastomer and PP macromolecules with polymeric bridging chain formed by bridging agent. The chemical structure of MS-PTPE was significantly affected by different proportion of elastomer, different dosage of initiator and different dosage of bridging agent, and there was a certain synergistic effect between the dosage of initiator and bridging agent.