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The review of the lithology of volcanic–sedimentary units, ages of ophiolite mélanges, magmatic and detrital zircon age spectra, as well as the whole-rock Nd and zircon Hf isotopic systematics, has led to the identification of three subduction systems in the West Junggar domain and one in the East Junggar domain. In West Junggar, it is from the south to the north: (1) a north-dipping Carboniferous system consisting of the West Karamay accretionary wedge, the Darbut and Karamay ophiolite mélanges and the Toli magmatic arc; (2) a south-dipping system comprising the Cambrian Hebukesaier–Hongguleleng ophiolite mélange, the Silurian–Devonian Boshchekul–Chingiz arc and the Toli–Mayile–Tangbale Ordovician–Silurian back-arc; and (3) another north-dipping Carboniferous system including the Tarbagatay accretionary wedge, the Zharma–Saur arc and the Erqis Complex back-arc. By contrast, the East Junggar, from south to north, is defined by a north-dipping Devonian–Carboniferous subduction system consisting of the Jiangjunmiao accretionary complex, the Kalamaili ophiolite mélanges, the Yemaquan arc and the Dulate and Erqis Complex back-arc system that are separated by late Cambrian–Ordovician Armantai–Zhaheba ophiolitic mélanges. The structural data define the Carboniferous D1 folding and imbrication of Cambrian–Devonian crust of the Paleo-Asian Ocean, including accretionary wedges, arc and back-arc sequences and exhumation of ophiolite mélanges. Deformation D1 led to the north–south amalgamation of the West Junggar units and the orthogonal east–west amalgamation of the East Junggar units. The whole system was subsequently affected by the Permian D2 deformation, which caused further shortening of the West Junggar sequences and almost an orthogonal folding of the Carboniferous fabrics in the East Junggar. D2 was accompanied by northward movement of the Junggar basement block, which generated sinistral wrench zones in the West Junggar and dextral transpressive zones in the East Junggar. The geophysical data showed a continuous magnetic and gravity high that corresponds with the Zharma–Saur and Yemaquan arcs, which warped around the Junggar Block promontory. The other gravity and magnetic highs are parallel to zones of imbrication of oceanic crust and exhibit a systematic dip to the northwest in the West Junggar and to the north-northeast in the East Junggar. These data allow us to correlate the East Junggar to the Tarbagatay–Zharma–Saur–Erqis subduction systems and attribute them to the Mongolian Collage. On the other hand, the West Junggar Boshchekul–Chingiz arc and Karamay–Darbut anomalies define the subduction systems of the Kazakhstan Collage. Altogether, the subduction of the Cambrian–Devonian Paleo-Asian Ocean played a significant role in the construction of the Kazakhstan Collage to the west and the Mongolian Collage to the north. The West and East Junggar Paleo-Asian subduction systems were further split due to the indentation of the Junggar Block. Such a kinematic model is well correlated with and evidenced by the analogue of the present-day Philippine Ocean system.