In order to develop appropriate reservoir protection measures in the northern margin of the Qaidam Basin and improve its oil and gas recovery efficiency, characteristics of clay minerals from eleven clay rock samples from the northern margin of the Qaidam Basin were investigated using X-ray diffraction analysis, the Scanning Electron Microscope (SEM) and energy spectrum analysis. Clay mineral composition and distribution characteristics of the main hydrocarbon reservoirs, I.e., from the Jurassic and Paleogene-Neogene, were explored. We analyzed the main factors which affected these attributes. The results show that the major clay minerals in the northern margin are chlorite, kaolinite, illite, smectite and illite/smectite inter-stratified minerals, Illite is the most widely spread clay mineral in this area.Chlorite is mainly found in the entire Neogene and in shallow horizons of the Paleogene. Smectite is enriched in the shallow Paleogene-Neogene. There are large amounts of kaolinite and illite/smectite inter-stratified minerals in the Jurassic. The major factors affecting the different development of clay minerals in the region are properties of parent rocks, paleoclimate and paleowater media conditions,diagenesis transformation, tectonic and terrain conditions.