Abstract: Under the international consensus that the novel coronavirus pneumonia and human beings coexist for a long time, the anti-epidemic Chinese medicine represented by Lianhua Qingwen has vividly practiced the new concept of "inheriting the essence, keeping the righteousness and innovation". Based on the latest policy situation, the thematic system of registration and patent protection of Chinese medicine has been covered, but there are still some practical dilemmas such as unsuitable innovation standards, low quality of patent value, as well as misalignment and disconnection of the system. Therefore, through the empirical analysis of the synergy between new drug registration and patent protection of Lianhua Qingwen, we propose the countermeasures for the construction of synergy between Chinese medicine registration and patent protection by exclusive examination of patent creativity, cultivation of high-value patents, as well as linkage of registration and patent protection system, hoping to provide practical reference for the high-quality synergy development of Chinese medicine industry with the new opportunity.