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Early Cenozoic rift basins developed commonly on the Mesozoic basement along the SE Asia Continent. However, Eocene–Oligocene sequences were only exposed widely onshore Taiwan. We study benthic foraminifera and determine U–Pb geochronology of detrital zircon grains in the Early Cenozoic sequence onshore Taiwan for understanding if there was any significant change in faunal content and sediment provenance between the Eocene syn-rift sequences and the overlying Oligocene post-rift strata across the breakup unconformity. The Eocene syn-rift sequences are mostly of thick, cross-bedded sandstones of fluvial-deltaic depositions without marine fauna. Intensive study on the Eocene stratigraphy in more than ten sections all over the Taiwan mountain belt in the last three decades, shallow marine benthic foraminifera of Gaudryina hayasakai-Hanzawaia asterizana-Planularia okinoshimaensis-Heterolepa praecinta assemblage were found only in very limited exposures in the Western Foothills, central Taiwan. This study shows that the Eocene benthic foraminiferal assemblage is similar to the Shihtsaoan fauna in the overlying Oligocene post-rift marine strata. This indicates no significant faunal break across the breakup unconformity. As a consequence, Gaudryina hayasakai Zone of the Shihtsaoan age can extend downward to the Eocene and the Shihtsaoan Stage would be equivalent to the Hsuehshanian Stage established previously from northern Taiwan. The Taiwan Eocene marine sequences could be deposited in a normal-fault bounded narrow seaway or gulf connecting southeastward to the open Huatung Basin. U–Pb geochronology of detrital zircons in the Taiwan Eocene syn-rift sandstones shows a prominent age peak centered in Yenshanian (100–155 Ma) similar to the Paleocene–Oligocene fluvial-deltaic deposits in the East China Sea and is also comparable to the U–Pb zircon age spectrum of modern river sands of the Fujian Province, SE China. Petrographic study also suggests a prevailing sediment provenance of the Cathaysia granites and volcanics. These Cathaysia detritals were transported to the Taiwan Eocene grabens through some SE-flowing rivers. Structural reconstructions in previous study indicated that the mountain belt with the Eocene sequences in NE Taiwan had been shortened by imbricated thrusting westward for 160–200 km wide during the arc-continent collision in the last 6.5 Ma. Integrating paleontology and sedimentology evidence reveal that the Eocene coast was located along the modern shelf break of the East China Sea ~ 350–400 km east off the modern Chinese coast line. This implies that in the Eocene time (~ 40 Ma) there was no wide Asian epi-continental marginal seas off Chinese coast until the onset sedimentation of the Oligocene post-rift strata during opening of the South China Sea in the Early Oligocene time (~ 33 Ma). [ABSTRACT FROM AUTHOR]