Objective To investigate the distribution features and laws of small mammals and ectoparasitic fleas in different landscapes in domestic rat plague foci in Southwest Yunnan and their relationship with plague prevalence. Methods Yunxian, Yongde, Jinggu, Ninger, Menghai and Mengla were sampling area of our research. The systematic investigation on small mammals and their ectoparasitic fleas distributed in different landscape ecosystem were carried out. The characteristics of the spatial distribution of diversity of small mammals and their ectoparasitic fleas were analyzed using community ecological indexes. Results There were 719 small mammals captured, which belonged to 19 species (subspecies), 12 genera, 6 families and 3 orders. Rattus tanezumi (55.77%) were dominant species. A total of 229 fleas were captured, and they were classified into 14 species (subspecies) of 11 genera in 5 families. Xenopsylla cheopis (57.21%) and Ctenophtha lmus lushuiensis (17.03%) were dominated species. Diversity index and evenness index of small mammals and ectoparasitic fleas in different landscapes was, in descending order, forest area> agricultural area> residential area. But the order of dominance index was opposite. Shannon-Wienne's diversity index(H') of small mammals captured in forest area, agricultural area and residential area was 2.28, 1.60 and 0.16 respectively, and that index of ectoparasitic fleas was 1.97, 1.75 and 0.15 respectively. Conclusion Landscape played a dominant role in community structure of host animals and fleas. Forest area helped to keep natural focus in domestic rat plague foci. Residential area was an important environment of plague prevalence. Agricultural area might be an important channel of transmission and prevalence of plague. Agricultural area played a pivotal role in long-term preservation, prevalence and diffusion of domestic rat plague foci.