Affected by Tianshan uplift, the southern Junggar Basin has experienced multi-stage tectonic movements and formed many large-scale anticlines with zonal distribution. The key to hydrocarbon exploration is to accurately implement anticline traps. This paper is guided by the fault-related folds theory to tectonically interpret several seismic profiles in the southern Junggar Basin and then summarize the anticline types and their hydrocarbon accumulation characteristics. This paper showed that the southern Junggar Basin has a tectonic assemblage pattern of “multi-detachment layers and multi-phase superposition”. According to the superimposed shape of the anticlines, they could be divided into overthrust anticlines, compound anticlines and multiple superimposed anticlines, and the horizontal and vertical positions of the different types of anticlines are different. The hydrocarbon accumulating characteristics of the different types of anticlines are shown to be different. The highs of the overthrust anticlines and compound anticlines are stable, and the degree of exploration is relatively high. Although the degree of exploration of multiple overlapping anticlines is low, multiple layers can be exploited simultaneously in the process of oil development, with great hydrocarbon potential. The characteristics of hydrocarbon accumulation in the southern Junggar Basin are discussed in order to provide guidance for efficient hydrocarbon exploration.