We investigate the formation and deformation of transfer zones and their impact on sedimentation during multiphase rifting using a three-dimensional seismic dataset in the Baxian Sag, the onshore part of the Bohai Bay Basin, northern China. The fault system in the study area is dominated by two arcuate, opposing boundary faults, that is, the Niudong and Maxi faults, which form an S-type fault system which does not link together. The fault system and structural-stratigraphic features between the Eocene and Oligocene syn-rift sequences were distinctly different during the Palaeogene rifting. These differences allow us to identify the two-phase transfer zones: (1) a NW–SE-trending Eocene transfer zone linking the NW-tilted Baxian Block and the SE-tilted Raoyang Block , and (2) the N–S-trending Oligocene transfer zone forming along the central part of the S-type fault system between the two inward kinks, and linking S-tilted and N-tilted fault blocks. The two-phase transfer zones comprise transverse boundary fault segments and fault styles which are related to strike-slip motion. The strike-slip faults occurred in the sequence where the transfer zone formed. The transfer zones significantly influenced the syn-rift sediments, drainage catchments and reservoir properties during the periods when they formed, and the two-phase transfer zones represent favourable positions for hydrocarbon accumulation in the Eocene and Oligocene sequences, respectively.