This paper studied the species diversity and fauna distribution of chigger mites on small mammals in Yunnan province, southwest Yunnan. In total, 120,138 individuals of chigger mites were collected from 13,760 individual small mammals, and these mites were identified as comprising two families, 26 genera, and 274 species. Of the five zoogeographical subregions, the mite species diversity in subregions I and II was higher than that in subregions III, IV, and V. Four mite species (Leptotrombidium scutellare, Leptotrombidium sinicum, Leptotrombidium deliense, and Helenicula simena) were the most dominant species in the whole province. Several vector species of chigger mites co-existed in Yunnan, and L. deliense (a main vector of scrub typhus in China) was mainly distributed in subregions IV and V with lower latitude and average altitude whereas L. scutellare (also a main vector in China) was mainly distributed in subregions I, II, and III with higher latitude and average altitude. Some geographically widely distributed mite species were also the mites with wide host ranges and low host specificity. The dominant mite species and their clustering tendency in the dendrogram of hierarchical clustering analysis were highly in accordance with the zoogeographical divisions. The species diversity of chigger mites showed a parabolic tendency from the low altitude (<500 m) to the high altitude (>3,500 m) along the vertical gradients and reached the highest value in the middle altitude regions in 2,000-2,500 m. The highest species diversity of the mites and their small mammal hosts happened in the regions around the Hengduan Mountains, which is a hotspot of biodiversity in Asia continent. The host and its sample size, geographical scope, landscape, topography, and some other factors comprehensively influence the species diversity and faunal distribution of chigger mites. A systematic field investigation with a wide geographical scope and large host sample is strongly recommended in the fauna study of chigger mites and other ectoparasites.