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In multi-phase rift basins, the links between fault activities and sequence stratigraphic architectures are still poorly understood compared to single-rift basins. The purpose of this work is to give implications for tectono-stratigraphic signatures in multiphase rifts based on seismic data from the Zhu-3 Depression in the Pearl River Mouth Basin, China. Stratigraphically, three composite sequences (CS1-3) defined by major unconformities in the Paleogene successions of the Zhu-3 Depression are interpreted, with each one subdivided into two or three third-order sequences. Regional unconformities and basin configurations indicate two episodic rift phases, termed rift phase 1 (formed CS1), and rift phase 2 (formed CS2) followed by a lithospheric breakup phase (formed CS3). From rift phase 1 to rift phase 2, the basin evolved from small-sized, independent half-grabens into relatively large-scale grabens and finally a dish-like basin configuration. Fault displacement and stratigraphic stacking patterns revealed three distinctive structural stages of rift phase 1: rift initiation (WC-SQ1), rift development (WC-SQ2), and rift termination (WC-SQ3) stages. However, an immediate decrease in fault activity was recorded in the rift phase 2. Immediate strain localization under rotated extension fields during episodic rift phases led to variabilities in tectono-stratigraphic architectures. In turn, this transition may likely contribute to interpreting the depositional pattern from balanced infill during rift phase 1 to an overfilled pattern during rift phase 2 as well as the breakup stage in response to possible enhanced sediment supply. This work enhanced our understanding of additional hydrocarbon evaluations in the Zhu-3 Depression, South China Sea. • The Eocene-Oligocene sequence framework in the Zhu-3 rift are systematically reported. • Fault pattern, basin geometry and drainages basin in episodic rift phases are illustrated. • Tectono-stratigraphic signatures of three rift cycles in the Zhu-3 rift are proposed. • Controls of boundary fault arrays evolution on two-phase rift development are discussed. [ABSTRACT FROM AUTHOR]