[Objective] Scutellaria baicalensisGeorgi is the third-class conservation of wild medicinal species. We used habitat suitability assessment model to divide the suitable habitat because this information could provide scientifical support for the conservation and sustainable utilization of resources.[Methods] Entropy weight and matter element model were used to determine the fuzzy membership function of baicalin content and 15 assessment factors. The entropy evaluation method was used to determine the weight of each factor. Finally, we estimated the spatial distribution ofS. Baicalensisby GIS spatial analysis in China.[Results] The area of unsuitable, less-suitable, moderately-suitable and high-suitable habitat for S. baicalensis was 5.07×10⁶, 1.65×10⁶, 1.88×10⁶ and 1.00×10⁶ km², respectively. The high-suitable habitat are mainly located in the north of Qinling Mountains-Huaihe River line, significantly Henan, Shandong, Liaoning, central and southern of Shaanxi, Hebei, Jilin, southern of Heilongjiang and Shanxi. In addition, there were some distribution in Yunnan, Anhui Province and other places, which was highly consistent with the actual distribution range.[Conclusion] Among all selected factors, mean diurnal range(MDR), precipitation seasonality(PS), precipitation of wettest month(PMAX) and aspect(ASPE) are the main control factors.