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The Sunda Shelf plays a key role in the sedimentation of the southern South China Sea (SCS). However, the impact of past climate changes on sediment transfer to the Sunda Shelf and the southern SCS is still unresolved. Here, we present new data on grain size, clay mineralogy, and Sr‐Nd isotopes of three marine cores, river sediments, and surface sediments of the Sunda Shelf. The results indicate that clay fractions of the central Sunda Shelf and the Gulf of Thailand derived mainly from the Mekong River and the rivers of northern Thailand since the last deglaciation. Significant changes in sediment sources are observed at 7.5 cal ka BP. From 13.3 to 7.5 cal ka BP, sediments in the Gulf of Thailand mainly originated from the rivers of northern Thailand, with contributions from the Mekong River increasing after 7.5 cal ka BP. An opposite shift is observed in the central Sunda Shelf. Such variations in the spatial distribution result from a combination of sea level and East Asian monsoon effects. After 7.5 cal ka BP, less Mekong River sediments were transported southeastwards into the southern SCS, and more sediments were gradually trapped within the delta and transported in a southwesterly direction into the Gulf of Thailand due to intense East Asian winter monsoon, which forced a strong southwestward coastal current. Our results demonstrate the important impact of East Asian winter monsoon strengthening and sea level rise in the mid‐Holocene, which can change sediment sources and transport processes on the Sunda Shelf. Sea level and monsoon are two important factors controlling sediment transfer in the tropical and subtropical continental marginal seas. However, the impact of past sea level and monsoon changes on mineralogical composition and sediment transfer to the Sunda Shelf (the largest low‐latitude continental shelf) and the southern South China Sea (SCS) is unclear. This study provides new data on grain size, clay mineralogy, and Sr‐Nd isotopes of sediment from marine cores, river sediments, and surface sediments of the Sunda Shelf to constrain sediment sources and climatic control on sediments deposited on the Sunda Shelf since the last deglaciation. We find that the Mekong River and the rivers of northern Thailand are two major sediment sources to the Sunda Shelf. An opposite shift of sediment sources at 7.5 cal ka BP is observed between the Gulf of Thailand and the central Sunda Shelf, which results from the transfer of the Mekong River sediments between the southern SCS and the Sunda Shelf caused by sea‐level rise and East Asian winter monsoon strengthening in the mid‐Holocene. Our results highlight that sea level and East Asian winter monsoons can significantly change sediment sources and transport processes on the Asian low‐latitude continental shelf. Clay minerals and Sr‐Nd isotopes identified sediment sources to the Sunda Shelf since the last deglaciation as Mekong and Thailand riversEstimation of the Mekong and Thailand river inputs to the sedimentation of the Sunda Shelf and the southern South China SeaSea‐level rise and East Asian winter monsoon strengthening drove major sediment‐source changes on the Sunda Shelf at 7.5 ka BP Clay minerals and Sr‐Nd isotopes identified sediment sources to the Sunda Shelf since the last deglaciation as Mekong and Thailand rivers Estimation of the Mekong and Thailand river inputs to the sedimentation of the Sunda Shelf and the southern South China Sea Sea‐level rise and East Asian winter monsoon strengthening drove major sediment‐source changes on the Sunda Shelf at 7.5 ka BP