With the purpose of exploring the widely distributed Mesozoic granitoids in SE China and the related mineralization, we carried out a new 530-km-long seismic wide-angle reflection and refraction (WARR) profile along the transect Wanzai- Hui'an. Based on a previous exploration in 2012 and the analysis of this WARR profile, we have deduced a detailed P-wave velocity model of the crust and uppermost mantle. The main results are: (1) The crustal thickness is about 30 to 32 km beneath the Yangtze Block and West Cathaysia, and 29 to 30 km below the East Cathaysia, which represents a significant thinning with respect to the worldwide average thickness of shields and platforms. (2) The variation in seismic velocity between the upper crust and middle-lower crust in the Yangtze Block and the Cathaysia Blocks indicates that the Shaoxing-Jiangshan-Pingxiang Fault (SJPF) is the tectonic boundary between the Yangtze and Cathaysia and the Zhenghe-Dapu Fault (ZDF) is the tectonic boundary between the west and east Cathaysia. (3) The middle crust exhibits a low P-wave velocity layer of 6.2 km/s below the Wuyishan Metallogenic Belt (WMB). This low velocity layer can be attributed to the delamination during the Caledonian orogeny and the Yanshanian extension. (4) The middle-lower crust shows a clear lateral velocity variation from west to east in Cathaysia. The subduction of the Paleo-Pacific plate is believed to be the main reason for the extensional tectonic environment and magmatism during the Yanshanian (Jurassic-Cretaceous) period, leading to significant crustal and lithospheric thinning. Relatively high velocity in the middle-lower crust and widely disseminated Cretaceous volcanic rocks in East Cathaysia may be related to the slab rollback of the Paleo-Pacific plate in the late Yanshanian (Cretaceous) period.