Abstract: As an important part of the intellectual property system, Geographical Indication plays an important role in the process of intellectual property protection of Genuine Medicinal Materials. In order to verify the protection effect of Geographical Indication and promote the realization of the strategic goal of building Yunnan Province into the largest Genuine Medicinal Materials center in China, the current situation of the protection of Geographical Indication of Genuine Medicinal Materials in Yunnan Province was studied and analyzed. The author found that in the process of protecting the Geographical Indication of Genuine Medicinal Materials in Yunnan Province, there are still some problems, such as the right confirmation mechanism to be improved, the supervision authority to be chaotic, the legislative protection system is not sound, the infringement relief system to be not perfect, the information platform construction to be strengthened and the brand building planning is not comprehensive. In order to improve the protection level of Geographical Indication of Genuine Medicinal Materials in Yunnan Province, the author suggests that the improvement should be made from improving the right confirmation mechanism of Geographical Indication, optimizing the management functions of centralized departments, promoting the construction of local legislative protection system, perfecting the rights protection assistance and relief system, speeding up the construction of information platform and strengthening the construction of Geographical Indication brand.