Physical-layer network coding (PNC) can effectively improve wireless networks by extracting superimposed signals and transforming collision’s dilemma into an advantage. The proposition of higher layer methods (such as Data Link and Network Layer) explicitly designed for PNC can better enhance wireless network performances. Since the field of PNC is very vast and has several applications, the researchers of the higher layers find it very difficult to propose a suitable PNC system for their research, which has led to the scarcity of research works of this type. This article proposes a new classification method designed to help researchers choose the optimal method that suits their system. This paper is a complete guide for researchers of higher layers to discover the PNC field and improve wireless network performances.