Climate in China has fluctuated greatly for last two thousand years. Also, the temperate-subtropical transition zone, as well as the distribution boundaries of subtropical biology and growth of suitable areas appear north-south lapse. In historical period, significant climate change will also be bound to the changes of the medicinal organism distribution suitable areas. The past dynasties herbal herbs have documented origin in detail, especially genuine medicinal materials producing areas. In this paper, Alisma orientale and Citrus aurtantium as examples, were used to elaborate the impact of climate change fluctuations on genuine producing area by evolution and change of genuine producing areas. The results showed that medicinal species were more sensitive to climate change such as A. orientale and C. aurtantium, its main producing areas or genuine producing area from north to south shifted in the Ming and Qing dynasties, consistent with the characteristics of climate change in China in last two thousand years. Factors prompted producing areas southward are not only low temperature and cold damage, and temperature and humidity have often synergistic effect. The human activities are more likely to exacerbate the impact.