The development of trench-arc-backarc (TABA) systems is uniquely associated with modern-style plate tectonics on Earth. The Qilian orogenic belt in NW China records the evolution history of the Proto-Tethys Ocean at the transition time from the Proterozoic to Phanerozoic. This paper presents systematic studies of petrography, U-Pb chronology and geochemistry on various rocks from a MOR-type ophiolite belt, active continental margin and back-arc basin in the Qilian orogenic belt to address the development of a modern-style TABA system. Arc magmas include felsic intrusions with ages of 530–477 Ma and felsic-mafic arc volcanic rocks with ages of 506–439 Ma, showing distinctive features of typical magmatic rocks formed at an Andean-type continental margin. The back-arc basin is recorded by a 490–448 Ma SSZ-type ophiolite with boninite, and Silurian turbidite flysch formation. We establish a three-stage tectonic history from the initiation of subduction to the formation of a mature Japan-Sea-type back-arc basin at the active continental margin in the Early Paleozoic era. (1) Northward subduction of Proto-Tethys Ocean initiated and the Andean-type continental arc developed at ~530–500 Ma with continual crustal thickening; (2) a tectonic transition occurred from an Andean-type active continental margin to a West Pacific-type active continental margin at ~500–490 Ma with rapid thinning of crust to ~35 km, and (3) mature ocean basins and back-arc-basin (BAB) ophiolites were formed in the back-arc extensional environment at ~ 490–450 Ma.