Cultural diversity is just as essential to humankind as biodiversity is to nature, and ethnicity can be used as a rich and concise measurement of cultural diversity. There are a variety of ethnic minorities in Southwest China. During the long history of complex ecosystem development, the ethnic groups in Southwest China have formed many excellent cultural traditions and unique ecological awareness. However, with the deepening modernization of ethnic areas, as well as rapid social transformation, population migration, and cultural changes, ethnic culture that is rooted in social history and traditional customs is suffering from unprecedented change and erosion, which has resulted from the excessive pursuit of economic growth and short-term benefits. Accordingly, studies of cultural diversity in Southwest China have attracted the attention of interdisciplinary scholars. In the present study, the cultural diversity of county-level administrative regions was quantitatively measured using the Shannon-Wiener Index, and dynamic changes among the regions in 1990, 2000, and 2010 were compared to characterize the spatiotemporal distribution of cultural diversity. The cultural diversity of Southwest China exhibited clear spatial heterogeneity, with lower diversity observed in the northwest part of the region and higher diversity observed in the southeast part. In addition, even though cultural diversity increased to a certain degree in the time series, cultural diversity was relatively low at the county scale. However, cultural diversity also increased with the expansion of spatial scale, which demonstrated that ethnic groups tended to live together at large scales but were inclined to cluster together at small scales. Spatial differences in cultural diversity were also observed when using the Theil Index at the province scale, with total and local differences among provinces decreasing over time, and the modified Morisita-Horn Index, which was used to assess similarities of ethnic composition, revealed that the similarity of provinces increased over time. Together, these results indicated that the distribution of ethnic groups in Southwest China was more blended and that ethnic integration has become a trend from 1990 to 2010. Further analysis, using ArcGIS 10.2, also indicated that the distribution of cultural diversity was closely related to the average slope of the distribution areas of ethnic groups in context of Southwest China's ecological environment. The social history and main causes of ethnic integration, reasons for the high cultural diversity of the stepped transition zones, and protection of Southwest China's traditional culture were discussed as well. The present study investigated the spatiotemporal distribution of cultural diversity underlying ecological factors in Southwest China and highlighted the importance of preserving and promoting the splendid cultural traditions of ethnic groups under the premise of respecting the nature. Thereby, it provided a useful reference for the sustainable development of the ecological environment and the construction of ecological civilization in Southwest China.