The three-dimensional positions of Paleozoic strata in the South Tianshan orogenoic belt were changed architecturally during the collision between the Tarim and Yining paleo-continents. With the measurement of an integrated geological-structural section as the hinge, the authors integrated the structural analysis, sedimentary sequence analysis and micropaleontologic study to study the stratigraphic sequences and ages of the Alatag Formation and the Qagan Shala ore-bearing rock series. Two new progresses have been made. Firstly, the Alatag Formation is a cycle of unidirectional successive deposition, with volcanic rocks predominating in the lower part, the ratio of carbonate/chert increasing progressively and grains of clastic rocks becoming coarser upward, and its age ranges at least from Early Devonian to Late Devonian (possibly to Carboniferous). Secondly, Silurian allochthnous bioclastic limestone and Silurian-Carboniferous autochthnous strata are exposed in the Qagan Shala area, and ore-bearing strata occur in the upper part of turbidites, whose age is Middle to Late Devonian. Based on the above study, the authors propose the basic principles and main approaches used in the reconstruction of the stratigraphic sequences of the erogenic belt.