The arid area is a very special zone for arid evaluation because of little rain and fragile environment. The general drought index of better applicability need further argument so as to apply to the drought monitoring. This study region is first divided into districts such as the sub-region, including 4 mountain areas, 2 desert areas and 5 oasis areas,which are delineated for the Aksu River basin based on the DEM and land use types. In this study, the monthly precipitation and temperature data from 1961 to 2011 were used to analyze and compare the applicability of standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI) in each study area. It analyzed the gotten situation of drought and historical drought. The results show that SPEI with short time scale(1、3、6 months) can more exactly express the arid tendency than SPI, but it still have errors in expressing the real historical drought change.The SPI and SPEI with long time scale (12 or 24 months) can basically express the drought year,but the precision of two standardized drought indices in mountains still need further validation.