Abstract: The design of subway stray current protection is crucial for ensuring the safe operation of subway systems and extending the service life of equipment. However, the knowledge in this field is complex, and there are many disputes in the implementation of standards, leading to misunderstandings in design, application, and operation and maintenance in engineering practice. If these issues are not resolved, they will seriously affect the safety and reliability of subways; therefore, it is necessary to conduct in-depth research on these misunderstandings and propose countermeasures. The article extracts controversial concepts and phenomena in protection, analyzes controversial clauses in standards, simulates the process of stray current generation, propagation, and hazards by establishing a physical model, and combines typical cases to analyze the causes and impacts of misunderstandings from the perspectives of design, construction, and operation.