The Baiyun sag is a deep one developing on the slope of the Pearl River Mouth Basin. It occurs as a composite graben horizontally, and is composed of two sub-sags versus one low uplift. Vertically, the sedimentary architecture could be divided into three layers, i.e. the faulted layer on the bottom, the faulted-ductile stretching layer in the middle and the draping layer on the top. The main rifting stage of the sag is supposed to be characterized by ductile extension and thinning of the crust. The special deformation pattern is probably attributed to the fact that the Baiyun sag is located in the transfer zone of the pre-existing weak zone, which made the sag a strongly deformed area, characterized by the greatly thinned lithosphere and active magmatism. The highly rising mantle under the Baiyun sag should be an important mechanism responsible for the ductile deformation, which caused partial melting of the upper mantle. Upwelling to the upper crust and the sedimentary layers, the partial melting materials accommodated extensional strain and caused non-faulted vertical subsidence. Magma was collected under the transfer zone after the first stage of rifting, and transferred laterally in a direction perpendicular to the extension to the ENE and WSW parts of the sag and upwelled along the NW-trending basal faults, where WNW-trending shear faults developed in swarms. The faulting activity and sedimentation history of the Baiyun sag may have been affected by the ocean ridge jump around 24 Ma and the cessation of sea floor spreading around 16 Ma.