The effects of secondary alterations on the characteristics of the crude oil are sometimes greater than those of the organic matter sources and the heat maturity. In the geological history, the thermal alteration is one type of common secondary alterations that occur in the subsurface. In this paper, by simulating in the laboratory the thermal alteration of the oil from the southern Junggar Basin and analyzing the obtained data, two indexes, P/MP and (3-MP＋2-MP)/(9-MP＋1-MP) are shown to have a good correlation with the thermal alteration. Moreover, a chart which can be used to identify the thermal alteration degree is proposed. With this chart, the relative thermal alterations of oils from Huoerguos and Hiutubu oil fields were identified based on the methyl phenanthrene composition. The crude oil from Well Huo 10 in the Huoerguos oil field with a slight thermal alteration indicates that the oil field is most likely a native reservoir. However, the crude oil from Well Huoqian 1 and Well Huo 002 with a severe thermal alteration shows that they are most likely secondary reservoirs migrated from deep buried reservoirs. The crude oil from Wells An 5, Shinan 31, and Hu 2 with a normal maturity shows that they are native reservoirs.