Based on study of the component and its carbon isotope of natural gas samples from the J1b reservoir of Nanan-1 well, the J2-1 reservoir of Qi-34 well and the N1 reservoir of Du-87 well in the south margin of Junggar basin, we suggest that these natural gases are coal-related gas herein. But the natural gases sample data from the J1b reservoir of Nanan-1 well and the J2-1 reservoir of Qi-34 well are distributed at the region where natural gas originated from Type Ⅱ kerogen often locates in the Whiticar chart board. Natural gas carbon isotope and natural gas components show that, the secondary action should alter C1/C2+3 and δ13C1. In view of the geological background of south margin of Junggar basin, the genesis of unconventional natural gas from Nanan-1 well and Qi-34 well and Nanan 1 well is bacterial degradation, which resulted in C1/C2+3 increase and δ13C1 lightening, but the genesis of unconventional natural gas from Du-87 well is methane leakage effect. According to the distribution region of the unconventional natural gas, the different development direction of bacteria degradation gas and the coal-related gas leakage in methane component are pointed out. The research conclusion is a necessary supplement to the Whiticar chart board, and makes the Whiticar chart board more practical in the research work about natural gas.