Polymer blending or alloying is one of the important routes to realize its high performance and functionalization. PA66/PP blends maintain the excellent performance of PA66 and PP, and also improve the performance of their own deficiencies. However, the polar PA66 is incompatible with the non-polar PP. It is necessary to compatibilize the blends to obtain good performance alloy materials. At present, different monomers grafted PP are used as compatibilizer of PA66/PP blend. Although the graft copolymer can improve the interfacial compatibility of the blends, the graft ratio is a key factor affecting the comprehensive properties of the polymer blend, thus restricting the preparation of high performance polymer blends. In various compatibilized strategies of polymer blends, it is important to study the grafting or cross-linking reaction induced by electron beam irradiation between continuous phase and dispersed phase. In this paper, In order to obtain a good PA66/PP alloy, and resolve the incompatibility of polar PA66 and nonpolar PP, electron beam irradiation was used to compatibilize PA66/PP blends. The effects of irradiation on the microstructure and mechanical properties of PA66/PP blends were investigated. And the results show that the interface compatibility between PA66 and PP is improved through irradiation; the tensile strength, flexural strength and impact strength of the blends can be also improved at appropriate irradiation dose range. Therefore, electron beam irradiation compatibilize PA66/PP solves the problem that PA66 is highly incompatible with nonpolar PP, and is not ideal for composite performance. It is a new approach based on radiation processing for the preparation and structural performance regulation of high performance PA66/PP blends, and with a wide range of applications.