Taiwan’s doubly vergent orogen is a relatively young and active arc-continent collision caused by the convergence of the Eurasian and Philippine Sea Plates occurring along a complicated seismogenic plate boundary. This study aims to investigate the evolutionary and tectonic features of the retro-wedge, which is involved in uplifting and shortening the growth of the Taiwan orogen. We delineate three potential seismogenic structures: the Longitudinal Valley Fault (LVF), the Ludao–Lanyu Fault (LLF), and the Central Range Fault (CRF) along the convergent boundary by using seismic tomographic image and relocated seismicity. We first discovered a west-dipping backthrust of the CRF bounding on the eastern Backbone Range, which can be traced to a distance of 300 km from the north Hualien city to the southeastern offshore. The fault led to the development of a crustal scale pop-up structure and resulted in the formation of a doubly vergent orogenic wedge in the retro-wedge side. Thus, the generation of the basement-involved backthrust has been attributed to the indentation of the exhumed forearc mantle wedge and remnant forearc crust into the Backbone Range during collision. As a result, the plate boundary consists of two opposite vergent thrust systems of the LVF–LLF and CRF that developed during the collision, following the closure of the forearc basin of the North Luzon Trough and Longitudinal Valley from incipient to mature collision, respectively. Our results provide new tectonic features along convergent zone constraints for geodynamic models of arc-continent collision allowing investigations of current mountain building in Taiwan.