The geographical distribution characteristics of villages characterised by ethnic minorities are determined by the selection of the site when the village was initially established. The location of inherited and well-preserved minority villages must be exceptionally compatible with the natural terrain, with a logical relationship. Nonetheless, the issue of village location, which is directly related to the development of the features of the geographical distribution, has received little attention from scholars. The average nearest proximity index, Voronoi, kernel density analysis, proximity analysis, and the Geographical Detector (GeoDetector) were used to analyse the geographic distribution characteristics of villages and their correlation with terrain, as well as the difference between the influence of each terrain factor. The findings indicated the following. (1) The geographical distribution of minority villages in Fujian Province is of the agglomeration type, with a significant “mononuclear” feature, and the topography has a facilitating effect on the clustering distribution of villages. (2) The geographical distribution of minority villages in each city of Fujian Province coexisted with the agglomeration type and the dispersion type, and the role of topography in promoting the agglomeration-type distribution of villages was not affected by the distribution density of villages. (3) The site selection of Fujian-minority villages is characterised by medium altitude, moderate slope, sun exposure, and no obvious hydrophilicity. Minority villages are mainly located in areas with an elevation of 202–647 m; a slope of 6–15°; a flat land aspect with a south slope, southeast slope, or southwest slope; and distance of 500–1500 m from 5–20 m wide rivers of level 2. (4) The site selection of Fujian minority villages is influenced by various topographic factors, such as elevation, slope, aspect, river buffer, river width, and river level, among which river width has the most substantial effect. (5) All topographic factors have a two-factor enhancing relationship with each other, aspect and slope have the most substantial effect and play a dominant role in site selection. The research findings illuminate the internal logic of the geographical distribution differentiation of villages characterised by ethnic minorities, which is critical for promoting the protection of modern ethnic-minority villages.