The southern Tien Shan is a folded area with widespread Paleozoic nappes. The ensembles of nappes distributed in Uzbekistan, Tajikistan, Kyrgyzstan, and China are described, and their structural similarity and distinctions in different parts of the area are shown. Nappes of the southern Tien Shan occur on a passive margin of the Paleozoic Alay-Tarim continent. The lower nappes are composed of the passive margin rocks; the upper, of the Paleozoic Turkestan oceanic crust rocks and of rocks of an accretionary prism that occurred nearby the Paleozoic Kazakh-Kyrgyz microcontinent margin. The accretionary prism was formed during a long-term interval. In the Moscovian after the closure of the Turkestan oceanic basin and during the collision of the Alay-Tarim and Kazakh-Kyrgyz terranes the accretionary prism rocks were overthrusted onto the Alay-Tarim continental margin. The oceanic crust subduction was followed by the Late Carboniferous and Early Permian subduction of the Alay-Tarim continental crust beneath the Kazakh-Kyrgyz terrane. At that time a transverse shortening of the Alay-Tarim continental slope resulted in a tectonic decoupling of sediments and formation of the southern Tien Shan lower nappes.