The newly acquired long-cable multi-channel seismic (MCS) lines were used to study the crustal structure and extension in an NW-SE elongated 150 km by 260 km strip from the slope to the deepsea basin in the northern South China Sea (SCS). These profiles are of good penetration that Moho is recognizable in ~70% length of the lines. Seismostratigraphic interpretation and time-depth conversion were conducted. A power function D = atb + c was used in the time-depth conversion, which avoided the under- or over-estimation of the depths of deep-seated interfaces by cubic or quadratic polynomial functions. Contour maps of basement depth, Moho depth, crustal thickness, and crustal stretching factor were obtained for the study area. In the dip direction, the Moho depth decreases stepwisely from 28 km in the outer shelf southwards to 19, 15, and 12 km in the deepsea basin, with ramps at the shelf break, lower slope, and the continent ocean boundary (COB), respectively. Accordingly, the crustal thickness decreased southwards from 25 to 15, 13, and 7 km, respectively. Under the center of the Baiyun (白云) sag, the crust thins significantly to < 7 km. The crustal stretching factor βc was calculated by assuming the original crust thickness of 30 km. In the centers of the Baiyun sag, βc exceeds 5. Tertiary and Quaternary volcanic activities show a general trend of intensifying towards the COB. An important finding of this study is the along-strike variation of the crustal structure. A Moho rise extends from the COB NW-ward until the shelf break, about 170 km long and 50–100 km wide, with Moho depth < 20 km. This is called the Baiyun Moho Nose, which is bounded to the east, west, and north by belts of high Moho gradients indicative of crustal or even lithospheric faults. The doming of Moho in the nose area might be the cause of the W-E segmentation of the crustal and geological structures along the slope of the northern South China Sea, and the cause of the strong crustal stretching in the Baiyun and Liwan (荔湾) sags.