The unique geographical environment of Yunnan Province in China and large-scale waves of Han migration during the Ming Dynasty contributed to the emergence and development of the Biantun culture. The toponym is the carrier of the Biantun culture: it records the integration process between the Central Plains and native Yunnan cultures. Based on the GIS spatiotemporal analysis of toponyms in Yunnan, this study reproduced the settlement characteristics of Biantun toponyms (BTT) and the spatial development of the Biantun culture in the Ming and Qing Dynasties. In addition, we’ve developed toponymical landscape index to represent the degree of spatial integration between the BTT and ethnic minority toponyms in Yunnan and explore the spatial characteristics of the integration of Han immigrants and local ethnic minorities. The results show that the spatial distribution of the BTT is consistent with the site selection of the central plains immigrants station troops to open up wasteland in Yunnan during the Ming and Qing Dynasties, and the centroids of BTT spread to outskirts and intermontane area from central towns. In Dali, Kunming, Qujing regions, etc present the distribution characteristics of the mixed of BTT and ethnic minority toponyms, and a higher degree of Sinicization in the central urban areas. This study used GIS applications for historical and cultural research and established the connection among Biantun culture and spatiotemporal data. Exploring evolution of Biantun cultural development through the spatial characteristics of toponymical landscape can help adjust policies for he development and protection of the Biantun cultural resources.