AbstractThe northern South China Sea (SCS) margin evolved from the Mesozoic convergent to Cenozoic divergent continental margin, and thus, it developed on a heterogeneous crystalline basement with inherited Mesozoic structures. Pre‐existing structures and their interactions with rift faults have historically not been described or interpreted in the intensely stretched Baiyun sub‐basin. Large‐scale 3D seismic reflection data allow us to identify four types of Mesozoic tectonic fabrics within the basement and explain their genesis: (1) Thin, isolated and north‐dipping seismic reflections 1, interpreted as thrust faults representing orogenic processes. Tilted thick seismic reflections 2 are formed by reactivation of seismic reflections 1 during post‐orogenic extension, which are all related to the NW‐ward subduction of the palaeo‐Pacific plate. (2) Thin, isolated and shallowly dipping seismic reflections 3 and low‐amplitude, semi‐transparent and chaotic seismic reflections 4 represent the low‐angle thrust system and the associated nappe units, which are related to the shift from NW‐ to NNW‐ward subduction of the paleo‐Pacific plate. Subsequently, we investigate the structural interaction between Mesozoic intra‐basement and Cenozoic rift structures. Syn‐rift, post‐rift and long‐term faults are developed in Cenozoic strata, and quantitative statistical and qualitative analyses revealed two main types of structural interactions between them and underlying intra‐basement structures: (1) Rift faults develop with inheritance of intra‐basement structures, including fully and partially inherited faults. (2) Rift faults modify intra‐basement structures, although they are controlled by intra‐basement structures at an earlier stage. Finally, our results reveal the control of pre‐existing structures on the geometry of the Baiyun sub‐basin, especially the selective reactivation of NE‐trending shear zones (SR2), which are influenced by the regional stress field and the width and dip of the shear zones.