Knowledge of the crustal structure is important for understanding the tectonic framework and geological evolution of southeastern China and adjacent areas. In this study, we integrated the datasets from the TAIGER (TAiwan Integrated GEodynamic Research) and ATSEE (Across Taiwan Strait Explosion Experiment) projects to resolve onshore-offshore deep crustal seismic profiles from the Wuyi-Yunkai orogen to the Taiwan orogen in southeastern China. Three seismic profiles were resolved, and the longest profile was 850 km. Unlike 2D and 3D first arrival travel-time tomography from previous studies, we used both refracted and reflected phases (Pg, Pn, PcP, and PmP) to model the crustal structures and the crustal reflectors. In total, data from 40 shots, 2 earthquakes, and approximately 1,950 stations were used; 15,612 arrivals were selected among three transects. Using these data, we determined the complex crustal evolution since the Paleozoic era, involving the closed Paleozoic rift basin in central Fujian, the Cenozoic extension due to the South China Sea opening beneath the coastline of southern Fujian, and the on-going collision of the Taiwan orogen. The shape of the Moho, which also reflects the crustal evolution, can be summarized as follows: ~ 30 km deep to the west of Fujian, deepening toward central Fujian (~ 35 km), becoming shallower toward the Taiwan Strait (~ 28 km), deepening again toward the mountain belt of Taiwan (~ 42 km), and becoming shallower toward the Pacific Ocean (~ 10 km).