In order to reveal the characteristic and change spatial distribution of rodents and fleas in Junggar Basin, this study took the plague natural foci in Junggar Basin as the target area and calculated the ecological indexes of rodents and fleas in different geomorphic types based on the data collected from rodents and fleas samples. Based on the calculation results of ecological indicators in different administrative regions, Moran's I index, center of gravity model, ellipse of standard deviation and other analysis methods were used to explore the clustering characteristics of ecological indicators of rodents and fleas in different administrative regions and to conduct relevant research on the characteristic and change spatial distribution patterns of rodents and fleas. The results showed that:(1) With the ecological indicators analysis of rodents and fleas in different geomorphic types, the species diversity and ecological dominance of rodents and fleas were negatively correlated, indicating that the ecological dominance of rodents and fleas was not obvious in communities with high species diversity; geomorphy that favors rodent species diversity was positively correlated with flea species diversity, confirming that the number of flea (parasite) species was increasing if the number of rodent (host) species was increasing;; the similarity of rodent and flea communities in the low altitude area was greater than that in the middle altitude area, and the similarity coefficient q was opposite to Cody index.; (2) In the spatial clustering analysis of different rodents and fleas indicators, the univariate Moran's I index of the number of rodents, the number of meriones meridianus, and the evenness of fleas was greater than 0, and the P value was less than 0.05, showing a spatial clustering pattern. Univariate local spatial autocorrelation analysis showed that there were various clustering patterns for some rodent and flea indicators, among which the most typical clustering pattern was high-high clustering pattern. The bivariate Moran's I index of different rodents and fleas indicators were greater than 0, indicating that the ecological indicators of rodents might affect the ecological indicators of fleas; (3) After the spatial distribution difference of the same ecological indicators between rodents and fleas was compared with the method of center of gravity transfer and standard deviation ellipse, the distribution ranges of the evenness of rodents and fleas and the ecological dominance of rodents and fleas showed similarity, and the standard deviation ellipse of rodents was more westerly than that of fleas. In conclusion, this study can provide reference for the prevention of plague in the natural foci of plague in Junggar Basin.