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The Indian summer monsoon (ISM) rainfall feeds a vast majority of the densely populated Asian continent. A deep understanding of the ISM rainfall variations and the underlying driving mechanisms during the Holocene is essential to predict its future behaviors and formulate improved mitigating strategies under the context of global warming. It has been widely recognized that the ISM intensity declined from the early to late Holocene, with a mid-to late Holocene transition. However, the nature of hydrological changes during this critical transition still remains vague. In this study, hydrological changes in Southwest China during the mid-to late Holocene transition are reconstructed based on the molecular and compound-specific carbon and hydrogen isotopic compositions of leaf waxes (δ13C and δD of n-alkanes) from the Yanjiang peat deposit in western Yunnan. Results reveal two-phase changes of hydroclimate during the mid-to late Holocene transition in Southwest China. During the first phase (5.5–4.2 cal kyr BP), Southwest China experienced an abrupt drying as indicated by the pronounced increases in both δ13C and δD values of the C29 n-alkane (δ13CC29 and δDC29) by 2.2% and 26‰, respectively. The second phase (4.2–2.6 cal kyr BP) witnessed shortening in the duration of the ISM season without further aridification, as demonstrated by an increase up to 35‰ in the δDC29 values and moderate oscillations in the δ13CC29 values. Such a two-phase hydrological transition is likely to have been triggered by the changes in the summer solar insolation and amplified by the ocean-atmosphere interactions. The first phase is primarily modulated by the positive Indian Ocean Dipole mean state, while the second phase is mainly linked with a more El Niño-like mean state over the Pacific Ocean.