To predict suitable growing regions for Leonurus japonicus and to provide scientific sopport for the habitat conservation and the exploitation and utilization of germplasm resources under climate change conditions, this study combined niche and priority conservation models to assess the future potential distribution of L. japonicus in China. To this end, distribution points and samples of L. japonicus were gathered through online and field surveys. The Maxent model with optimized parameters was used for predicting the suitable habitats of L. japonicus at different stages, and the Marxan model was used to determine the priority of protected areas. The results showed that the highest temperature in the hottest month, the lowest temperature in the coldest month, the precipitation in the wettest month, the precipitation in the driest month, and altitude were the main environmental factors influencing the distribution of L. japonicus. Under the three climate change scenarios, the centroid of the suitable area of L. japonicus migrated northward, and the migration position tended to expand further northwest. In the future, there would be no significant niche differentiation of L. japonicus; the Marxan results showed that priority protected areas for L. japonicus were in southwestern central China, Lingnan, southern east China, and Guizhou. Overall, the results of this research can provide a strategy for the determination of priority protection areas for Leonurus japonicus in China.