The composition and distribution characteristics of biomarker compounds in crude oils from Gasikule oilfield and Youshashan oilfield in the south part of western Qaidam Basin (Zone A) and from Nanyishan oilfield and Youquanzi oilfield in the north part (Zone B) were analyzed with GC-MS technology, and the genetic difference of crude oils from Zone A and Zone B and its geological influencing factors were discussed. The results showed that the distribution of carbon number of n-alkane in crude oils from part shallow reservoirs of Zone A with high ratios of peak areas of pristine (Pr) to n-C₁₇ and that of phytane (Ph) to n-C₁₈ was incomplete, so that preservation condition of shallow reservoirs from Zone A was poor, and part crude oils were slightly degraded by microorganism.