Abstract: The proton therapy system has significant clinical advantages over traditional tumor radiation treatment equipment and is also far more complex in terms of system architecture. However, due to the large size and complexity of these devices, electromagnetic compatibility testing faces considerable challenges. To address these challenges, this paper studies the electromagnetic characteristics and working principles of various components in the proton therapy system, combines them with corresponding standard requirements, and delves into the difficulties and testing methods of electromagnetic compatibility immunity detection through actual repeated tests. Furthermore, the paper proposes testing key points for beam quality tests and provides references for the selection of emission sources and distance settings in radio frequency electromagnetic field radiation immunity testing. The paper also supplements and improves the descriptions of alternative methods in the standards and offers solutions and testing suggestions for issues such as the excessive thickness of cables in the proton therapy system and the lack of suitable fixtures in conducted anti-interference tests. The provision of these solutions offers more effective references for related staff during testing, helps address difficulties encountered in practical operations, and thus more effectively ensures the safety and effectiveness of proton therapy systems.