Drought simulation and prediction are of great significance to drought early warning. However, it is difficult to predict hydrological drought in data-scarce areas. To address this problem, Tarim River Basin was selected as a typical representative of the data-scarce inland river basin in China, we constructed a hybrid model by combining the complete ensemble empirical mode decomposition with adaptive noise and the long short-term memory method to predict hydrological drought from 2022 to 2100 based on CMIP6. The results show that meteorological drought has quasi-3-month, quasi-5-month, quasi-7-month, quasi-1-year, quasi-2-year, quasi-4-year, quasi-9-year, quasi-17-year and quasi-54-year cycles. Hydrological drought has quasi-3-month, quasi-5-month, quasi-6-month, quasi-1-year, quasi-2-year, quasi-4-year, quasi-9-year, quasi-29-year and quasi-32-year cycles. The components of meteorological drought and hydrological drought have significant correlations on monthly, interannual, and interdecadal scales, with correlation coefficients of 0.282, 0.573, and 0.340, respectively, and p values of 0.000. The hybrid model had a better prediction accuracy (R2 = 0.951, MAE = 0.131, NSE = 0.951, d index = 0.987) than previous studies. The trend of the hydrological drought index in the sustainable development model (SSP1-2.6) shows a trend of increasing severity with a rate of − 0.004/10 years from 2022 to 2100. And from the sustainable development model (SSP1-2.6) to the unbalanced development model (SSP5-8.5), the hydrological drought gradually becomes more serious. This study provides a new mechanism for predicting hydrological drought in data-scarce areas and is of great significance for the early warning of hydrological drought in this area.