China's drug patent term compensation system has officially been implemented, but numerous hot-button issues remain unresolved in practice. This paper delves into several key problems through specific case studies, offering reflections and recommendations on corporate patent strategy and term compensation application approaches. It begins by introducing the legal origins of the drug patent term compensation system, including practices in countries such as the United States, Japan, and Europe. Then, it elaborates on the legal framework of China's system regarding scope of application, compensation duration, calculation methods, and eligibility criteria. Subsequently, it focuses on analyzing practical operational challenges in China, such as the definition of "new drugs", the meaning of "one drug", whether claims encompass new drug technical solutions, and protection scope limitations, while proposing corresponding solutions. Finally, based on legal significance, it provides enterprises with multiple patent strategy recommendations and adjustments to new drug application strategies, aiming to help them better safeguard their rights under the drug patent term compensation system.