The study on the spatial variability of hydraulic conductivity is one of the hot topics in hydrogeology. However, the variation law of hydraulic conductivity in Ili-Kunes Valley is unclear yet, restricting the research on the formation evolves and resource evaluation of groundwater. In this paper, the geostatistics theory is used to analyze the spatial variability of the hydraulic conductivity of the Ili-Kunes Valley aquifer. The results showed that the hydraulic conductivity of the unconfined aquifer in the western plain of the Ili Valley obeys the normal distribution of Box-Cox transformation. The hydraulic conductivity of confined aquifer obeys lognormal distribution, and the variogram is consistent with Gaussian model. The Kriging optimal value theory was used to analyze the spatial interpolation. The results of the hydraulic conductivity interpolation showed that the hydraulic conductivity is on the high side in the west of Huocheng County, and the lowest in the north of Yining County. The hydraulic conductivity of the Kunes Valley is relatively stable. The hydraulic conductivity of confined aquifer showed that the hydraulic conductivity gradually decreases from east to west, except that the hydraulic conductivity is higher near Cha County. Combining the physiognomy and hydrogeological conditions in this area, the hydraulic conductivity division of unconfined and confined aquifer was divided, which provides a key hydrogeological parameter for the evaluation of the groundwater resources.