The Fergana Basin is a large depression in the southern part of the Tianshan Mountains. Controlled by basement faults and related tectonic activities, three tectonic layers are defined in the basin. The basement of the basin consists of strongly metamorphosed Paleozoic deposits by folding orogeny, and the middle tectonic layer is the sedimentary cover deposited in the stable phase of the tensional rift from Mesozoic to Paleogene, while the uppermost tectonic layer is the molasse deposits after the orogenic stage since Neogene up to the present. Three sets of source rocks have been found in the Basin, which include marine mudstone and marl of Paleogene, regional transgressive deposits of upper Cretaceous and lacustrine and swamp mud shale of Middle and Lower Jurassic. There are four sets of reservoir systems in the basin in Jurassic, Cretaceous, Paleogene and Neogene respectively. Both the regional and local cap rocks are well developed in the basin. Therefore, there occur effective source rock-reservoir-cap rock assemblage for oil and gas accumulation. In addition, under the control of tectonic deformation and depositional environment, three types of traps are available in the basin, i.e. the structural, structural-stratigraphic and stratigraphic traps. The distribution of oil and gas in the basin is finally dependant on the tectonic activities in early Quaternary. Torsional faults may destroy existing traps, and create a path for the hydrocarbon migration to the overlying reservoir rocks in Neogene. Of cause, it will cause heavy loss of hydrocarbon gas.