A large suite of lower crustal xenoliths from Cenozoic basaltic rocks from three widely spaced localities in the eastern part of the South China Block (SCB; Xilong, Qilin and Leizhou) and two localities (Nushan and Guizishan) close to the suture between the North and South China Blocks in Southeast China has been studied in detail. They are used to define the nature of the lower crust beneath these regions and to define two distinct types of lithospheric domains resulting from different tectonic episodes. Lower crustal xenoliths from the Nushan area have distinctive petrologic and geochemical (including isotopic) characteristics indicating formation by underplating of continental basaltic magmas around the crust–mantle boundary. Geochemistry of these granulites demonstrates that an isotopically enriched old source component had played a significant role in the formation of the Nushan xenoliths. The lower crustal xenoliths from the South China Block reveal different origins and source compositions from those from the Nushan area. The South China Block xenoliths are considered to be derived from the underplating of continental arc-type basaltic magmas, but also show evidence of significant assimilation and fractional crystallisation (AFC) that produced abundant cumulates and fractionated liquids with strong crustal contamination signatures. They are geochemically and isotopically similar to the outcropping Late Mesozoic gabbros and basalts in the same region and are inferred to be their underplated high-pressure analogues and products of AFC with the lower crustal sources parental to the more silicic Mesozoic outcropping magmatic rocks. These Mesozoic basaltic magmas from the South China Block are geochemically distinct from the Cenozoic basaltic volcanics in this region, indicating a secular source change from a continental arc setting to an intraplate extensional regime. This significant change from Mesozoic to Cenozoic may indicate eastward movement of the subduction zone of the Pacific Plate and/or increase of the subduction angle. The close affinity of the lower crust in the Nushan area with events and deep-seated crustal rock types from other domains in the North China Block (NCB), and the strong difference from those for the South China Block, indicate that the subsurface suture between these large-scale tectonic domains lies south of the Nushan area.