Study region: The Kaidu-Kongque River Basin (KKR), a typical inland river basin in Central Asia, is characterized by a "mountain-oasis-desert" composite ecosystem. Study focus: Utilizing long-term meteorological data from 1960 to 2023, standardized precipitation indices (SPI) and standardized precipitation-evapotranspiration indices (SPEI) were calculated across multiple timescales (1, 3, 6, 9, and 12 months). Drought breakpoints were identified using the Pettitt test, and the Modified Innovative Trend Analysis (MITA) method was employed to uncover the spatiotemporal patterns of meteorological drought (as indicated by SPI) and hydro-temperatural coupled drought (as indicated by SPEI) within the KKR Basin. Additionally, the diagnostic capability of the MITA method in capturing nonlinear drought trends and breakpoints was validated, addressing the limitations of traditional methods. New hydrological insights for the region: The significant spatiotemporal divergence of drought is evident: spatially, a "west-east differentiation" pattern emerges-drought intensifies in the western plains (Korla, Yuli) as indicated by rising SPI/SPEI values, whereas the eastern highaltitude area (Bayinbuluk) shows signs of humidification but an increase in the frequency of extreme drought events. Temporally, abrupt changes in SPI (1980-1987) occur earlier than those in SPEI (1996-1999), with 1999 marking a critical transition period; high-altitude areas display scale specificity, with non-significant SPI-3 mutations (p = 0.62) but concentrated mutations at other scales in 1999. Enhanced drought persistence is indicated by SPEI, which shows stronger drought persistence than SPI. The 12-month SPEI (SPEI-12) has a longer duration than the corresponding SPI, and since 1990, summer drought durations have been significantly prolonged, increasing the risks of long-term impacts. The MITA method provides a reliable drought diagnosis: it accurately identifies turning points in drought trends, quantifies the proportions of drought classes, and reveals the propagation from meteorological to hydrological drought, offering a dependable technical tool for drought monitoring in arid regions with complex terrain.