Typical reefs in the Paleogene and early Neogene strata of the Qaidam Basin, Tibetan Plateau, China, reveal their internal structures and sedimentation environments and consist mainly of algal reef, stromatolite reef and thrombolite reef with distinct reef structures, fore-reef, back-reef and reef-plateau. The fore-reef is characterized by a combination of pinnacle reef, thrombolite and algal reef. The back reef is composed of stromatolite reef and algal reef. The pinnacle reefs (micro-atoll), most of which are several tens of centimeters in diameter (whereas some exceptionally big ones are over 200 cm in diameter), and several tens of centimeter to 2 m in height, are situated on the far front-edge of the reef; the pinnacle reef is also often of recumbent form with a gravel-filled circular hole in the center. The algal reef is in the form of dome and irregular beds, and filled with algal detritus, ostracodes, spirorbis fossils, ooid and terrigenous debris, and worm traces; cavities and scour marks are often developed. The algal reef is gray commonly when fresh and weathers to a brown color. The lacustrine thrombolite in the Qaidam Basin is light gray or deep gray when fresh, white-gray or brown when weathered, dense and homogeneous with abundant pores filled by oil and bitumen. Observed under the microscope, the thrombolite consists mainly of brown or brown-black clots with a little algal debris, ooid, pellet, ostracodes, spirorbis fossils and terrigenous debris, in some cases, terrigenous debris, even gravel, is abundant. Many features of the thrombolite suggest that it is formed in a high-energy envkonment. The stromatolite reefs developed on the lacustrine algal reef in the Qaidam Basin are very complex whether in shape or in internal structure. The simplest ones form laminated layers and the most complex ones have intensely branching structures. The size is also variable.