The richness and uniqueness of natural conditions make Southwest China a hot spot for biological diversity. There is also a long history of traditional customs and colourful ethnic culture in Southwest China, owing to the presence of several ethnic minorities. Both biological and cultural diversity are the basis for conserving the natural world and human societies. Considered as the sum of differences in the world, biocultural diversity refers to the complex connection between these two forms of diversity, and increasing attention is now being paid to this concept. Southwest China is the ideal region to study spatial patterns of diversity and the factors influencing them, but little quantitative research exists. Thus, we used 603 administrative districts at the county level to quantitatively calculate biocultural diversity, to identify any spatial patterns, and to analyse how different factors influence spatial distribution of this diversity. Cultural and biological diversity differed slightly in spatial distribution, but many high-value or low-value clustering areas overlapped. Among them, the Hengduan Mountains, as well as the lower reaches of the Lancang River Basin and the Yuanjiang River Basin, were high-value clustering areas for cultural and biological diversity. Low-value clustering areas included the upper reaches of the Yalu Tsangpo River Basin, the Nujiang River Basin, and the Sichuan Basin. In addition, high biocultural and biological diversity had similar regional distributions, as did low biocultural and cultural diversity. Overlapping effects of high-/low-value clustering areas for both variables resulted in a blanket pattern of biocultural diversity. Owing to terrain conditions and human disturbance, the three forms of diversity, viz., cultural, biological, and biocultural, all tended to change from "low to high" or "low to high to low" along the course of the rivers within watersheds. Analysis of influencing factors demonstrated that cultural and biological diversity played a mutually reinforcing role to each other. Moreover, average slope strongly affected the distributions of cultural, biological, and biocultural diversity. Highly diverse areas tended to be those with steeper slopes, larger altitude, and slope variation, but lower water coverage. The close connection between cultural and biological diversity was reflected in geographical overlap. We conclude that diversity conservation in Southwest China should consider both cultural and biological diversity. More research and protection practices should be implemented to better understand biocultural diversity.