Based on the geologic interpretation of Landsat TM images covered the southwestern margin of Junggar Basin, and integrated with the geologic data obtained from the geologic field survey and the results of BSS JGIsimulation for hydrocarbon generation and expulsion of source rocks, this paper analyses the neotectonic deformation character of the second and third row thrust-fold zone since the end of Pliocene, formation age of anticline and thrust structures, and the relationship of neotectonic movement with oil and gas. The research results show that neotectonic deformation of the second and third row anticline zone is very intensive, their deformation starts in the end of Pliocene, the neotectonic deformation is the most intensive in the end of early Pleistocene, the second and third row anticline zone has formed in the early stage of middle Pleistocene, the peak time of hydrocarbon expulsion for the favorable source rock-Anjihaihe Fm. is later than the formation age of these anticlines. The oil and gas from Anjihaihe Fm. is probably accumulated in these anticlines. The thrust faults usually develop near the core or in the northern limb, on one hand, they provide the pathway for vertical migration of oil and gas, on the other hand, they also cause the loss and destruction of oil and gas.