The Zhu 3 Depression is located at the transition between the South China Sea and the South China Block. The Cenozoic structure reflects the dynamic background of the South China Sea. We used 3D seismic and log data to study the structural evolution of the Zhu 3 Depression. We defined the characteristics of Cenozoic rift deformation and the migration of the depocentre based on fault activity and the distribution of sediment thickness. The spatial and temporal differences in the Cenozoic structure of the Zhu 3 Depression are due to the influence of pre-existing faults and regional stresses. Our results show that there are three populations of faults in the Zhu 3 Depression, striking NE, east–west and NW. The NE-striking faults are mainly large-scale boundary faults. The east–west-striking faults are small and were activated in the later stages of deformation. The NW-striking faults are continuous at depth, but are en echelon and parallel to each other at shallow depths. Based on these results, we suggest that the NE- and NW-striking pre-existing faults divide the Zhu 3 Depression into different structural zones and controlled the differences in deformation in the basin. The regional stress direction, which is controlled by regional plate interactions and the Red River Fault Zone, changed clockwise from NW-trending during the Paleocene to NE-trending during the Mid-Miocene. These findings will contribute to a better understanding of the evolution of the entire South China Sea. Thematic collection: This article is part of the Emerging knowledge on the tectonics of the South China Sea collection available at: https://www.lyellcollection.org/topic/collections/south-china-sea