The forming of large rivers are the integral consequences of the deep earth process and the surface. In contrast to the hot topics for rivers related to orogenic domains, rift-related large rivers are largely ignored especially in deep time studies. The Cenozoic East Asia margin provides very good opportunity to observe this kind of rivers. It has been believed that basin-and-swell physiography dominated the East Asia margin and impeded the forming of large rives in the early Cenozoic. In this paper, we combined provenance analysis of East China Sea Basin, where is a crucial place to trace the river evolution in East Asia margin, and regional geologic constraints to reveal drainage reorganizations. Detrital zircon U-Pb ages from the Early Eocene sediments of the East China Sea Basin are firstly reported. Our results together with literature data demonstrate that regional provenance changes occurred at the middle Eocene from one singe age peak at ~110 Ma of proximal sources to multiple age spectrum derived from far inland. Source to sink analysis indicated that the North China Block and Korea Peninsular provided the most detritus. Sedimentation and tectonic features of rift basins in the potential source areas indicated that rivers flowed into Bohai Basin and Jianghan Basin cannot provide terrigenous clasts for the lower reaches in the Eocene. Contrastingly, the dominantly fluvial sediments across the Subei-South Yellow Sea Basin suggested external river system and a bypassing region since the middle Eocene, coinciding with provenance change in ECSB. All these demonstrated that a large river (East Asia River) established in east Asia margin in the middle Eocene and flowed southwestward approximately 1500km to the sea in southern ECSB. This river might last to the middle Miocene. The deep earth processes driven by Izanagi-Pacific ridge subduction resulted in the overfilled stage of Subei-South Yellow Sea Basin and the post-rift subsidence in west depression of ECSB, and thus facilitated the initiation of the EAR. Our finding shed new light on the evolving landscape in East Asia and showed how subduction of deep earth process controlled the initiation of rift-related large rivers.