We integrate previous work on the Hegenshan–Heihe suture with our interpretation of geomagnetic anomaly and seismic reflection data to investigate the role of the Hegenshan–Heihe suture in the evolution of late Mesozoic extensional structures in the Wunite depression of the Erlian Basin. Sags in the Wunite depression present as NE50° trending in the western sector, N0°–NE30° trending in the central sector and NE45° trending in the eastern sector. Our results highlight the importance of the pre-existing Hegenshan–Heihe suture in the evolution of the late Mesozoic rift system and reveal the following details. (1) The NE50° extent sags in the western sector are controlled by the c. NE50°-trending suture. Moreover, the extensional deformation of the reactivated suture during Early Cretaceous time resulted in a further vertical and horizontal extension of major border faults. (2) The N0°–NE30° extent sags in the central sector are influenced by the c. NE75°-trending suture. The sinistral strike-slip component of the reactivated suture during Early Cretaceous time resulted in a strike rotation of major border faults from NEE-trending (following the suture) to NNE-trending. (3) Because of strike-slip deformation, which resulted from the deformation of the reactivated suture accrued in major border faults, light dip-slip deformation led to less vertical offset. (4) The NE45°-trending sags in the eastern sector are controlled by the c. NE45°-trending suture. Moreover, the extensional deformation of the reactivated suture during Early Cretaceous time facilitated a further vertical and horizontal prolongation of major border faults.