To decipher possible crustal modifications associated with complex tectonics in SE Asia, we have conducted a systematic receiver function investigation beneath the central Sunda plate mainly including Borneo, the Malay Peninsula, Sumatra and part of the South China Sea (SCS). Well-determined observations from a total of 22 stations reveal a laterally heterogeneous crust with thickness ranging from 22.8 km to 39.1 km and Vp/Vs values varying from 1.68 to 2.12. An increasing pattern of Vp/Vs ratios towards the Sumatra fault and the Toba Caldera indicates significant modifications of crustal composition possibly due to melting from the Indo-Australian subduction. Crustal compositions beneath the Malay Peninsula are determined to be mostly felsic to intermediate rocks. Crustal thinning at the Sibumasu terrane relative to the East Malay block is revealed and may be attributed to joint effects of Late Paleogene rifting and a subsequent thermal anomaly. The southwards subduction of the hypothetical Proto-SCS may have contributed to the revealed magma intrusion and thinned crust beneath NW Borneo, and developed an accretionary setting at NE Borneo. The cessation of the Proto-SCS subduction further promotes collision between NE Borneo and Nansha block, which is supported by the observed crustal thickening. Thinned crust at the southern margin of the SCS basin is further confirmed as continental in origin and has been altered by possible post-spreading volcanisms.