Da Qaidam Salt Lake, northern Qaidam Basin, is known for its liquid and solid boron resource. More than that, pinnoite bearing sediments, occurring in this lake, are rare in the world. However, little attention has been paid to the ore-forming environment and minerogenetic mechanism of this special borate deposit. The study analyzes high resolution subbottom sediment profile DCD-2 and DCD03 from Da Qaidam Salt Lake, through multi-index methods including lithostratigraphy, sedimentology, mineralogy, geochemistry and radiocarbon chronology, which aims to demonstrate the minerogenetic mechanism of pinnoite and other borate mineral deposits, and to provide contribution to the ore-forming theory of borate deposits in salt lake systems. The results show that subbottom pinnoite deposition commenced from 1790a BC with the content is 35 percent, and the content of boron oxide is approximately 3 percent to 16 percent which belongs to middle and low grade borate deposit. The content of ulexite and hydroboracite in lakeside is 82 percent and 35 percent respectively, and the content of boron oxide is approximately 3 percent to 9 percent which belongs to low grade borate deposit. The results indicate that Da Qaidam was not a salt lake before the pinnoite formed, and that the salinity and calcite began to increase with occurrence of gypsum, which represent a rapid transition into a sulfate type salt lake. The pinnoite deposit was formed in a salt lake environment. Pinnoite in subbottom as well as ulexite and hydroboracite in lakeside formed in the lake environment with specific hydrogeochemical conditions, and a set of borate mineral deposits finally formed due to different mineralizations and minerogenetic mechanisms in different zones. The forming of borate deposit was controlled by the inherent geochemical characteristics of boron and the external conditions, which is a coupling mechanism. The salt lake brine is weak alkaline to alkaline in the whole forming process of borate deposit. At last, we propose the specific minerogenetic mechanism of borate deposits in salt lake and establish the minerogenetic pattern of Da Qaidam Salt Lake, i.e. the high mountain-deep basin-shallow water pattern.