This study was conducted to explore the ecological factors that affect the fruit quality of Cinnamomum migao, a special seedling medicine in Southwest China, and to provide certain technical support, the theoretical basis for the site selection, cultivation and wild population tending. The results of total flavonoids, crude fat, total sugar, reducing sugar, polysaccharide, crude polysaccharide and soluble polysaccharide from 22 samples of C. migao fruits from different habitats were combined with 12 climatic factors and 11 soil factors to carried out the quality division of Migao by the collaborative Kriging method in the spatial interpolation function of AcrGIS. The results showed that 5 soil factors and 8 climatic factors had a significant effect on the quality of C. migao fruit. The areas suitable for chemical accumulation of Migao fruit are Baise, Liuzhou, Hezhou in Guangxi Zhuang Autonomous Region, Yunfu and Meizhou in Guangdong Province, etc. Comprehensively considering the factors, such as soil, climate, quality and yield of medicinal materials, it is suggested that the Hongshui River Valley zone at the junction of Guizhou and Guangxi with suitable climate and fertile land should be selected as the site for artificial cultivation.