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It is widely acknowledged that the growth and linkage of a boundary fault affects the evolution of the accompanying sedimentary basin and exerts a strong influence on its sedimentary characteristics. In this study, we attempt to discuss the evolution of a boundary fault and rift basin by using seismic interpretation, incremental fault throw, and growth rate–distance (G–d) profile, which are more suitable parameters than the expansion index in rift basins where footwall strata are missing because of erosion or a depositional hiatus. Therefore, the Gaoyou depression is taken as an example. The Gaoyou depression is the largest hydrocarbon-bearing depression in the Subei Basin, which is a representative rift basin in eastern China. The depression is bounded to the south by the Jiangdu–Wubao fault zone, which includes the Zhen 1–Wu 1, Zhen 2, and Wu 2 faults. Using high-resolution, three-dimensional seismic data, the Zhen 1–Wu 1 fault can be subdivided into four segments based on its G–d profile: the Shaobo, Fanchuan, Liuwushe, and Liulu segments. Growth rates indicate that the Zhen 1–Wu 1 fault and the Zhen 2 and Wu 2 faults developed successively from the Late Cretaceous to the Miocene during rifting of the Gaoyou depression and that development of the Zhen 2 and Wu 2 faults was controlled by the Zhen 1–Wu 1 fault. The four segments of the Zhen 1–Wu 1 fault were linked with each other by the time the Zhen 2 and Wu 2 faults formed in the Late Paleocene. An evolution model of the Gaoyou depression is set up in this study. Integrating the fault activity with previous sedimentological studies, we suggest that the evolution of the Gaoyou depression was controlled by the Jiangdu–Wubao fault zone rather than by a single fault. Successive slip of the Zhen 1–Wu 1 fault and the Zhen 2 and Wu 2 faults caused subsidence and migration of the depocenters. This study presents a case investigation of the effects of boundary faults on rift basins in eastern China.