It is hitherto first found home and abroad that the mineralized micron-sized biological spherical structure, sub-micron-sized biological granular structure and biological induced sheet organic structure are well preserved in the laminations of Miocene stromatlite in the western Qaidam basin. Combined with the recent study home and abroad, the micron-sized spherical structure is a kind of sulfate reducing microorganism similar with the Coccoid, and the sub-micron-sized granular structure is an important part of the EPS and may be the product of shrinking microorganisms under extreme conditions, and the sheet structure is the mineralized EPS and biofilm. Based on the analysis of the biological structure above and the crystals, such as quartz, salt and calcite, it can be confirmed that the formation of stromatolite in the study area may be through two processes, the organic active mineralization for the dark lamination and the inorganic in-situ precipitation for the light lamination, among which, the mineralization of the dark lamination may be furthermore divided into two phases: the photosynthesis within the upper enclosed acid micro-environment and the sulfate reduction and EPS mineralization by means of degradation in the lower semi-enclosed micro-environment, in contrast, the light lamination is mainly the product of in-situ inorganic precipitation with some influence from the organic matter preserved in the dark lamination during the lithofication.