There are abundant deep brine resources in the western Qaidam basin with good prospect of exploitation and utilization. However, previous studies have mainly focused on the western and northern Qaidam basin, and little is known about the occurrence and formation mechanism of deep brine in the central part of Qaidam basin. In this study, the deep brine samples from the Yiliping and the Xitaijinar salt lakes in the central Qaidam basin were investigated. The hydrochemistry and B isotopic composition of the deep brine samples obtained from deep drilling in this area were analysed, and the hydrogeochemical characteristics of the deep brine in the central Qaidam basin were clarified and the origin of the deep brine is discussed. The analysis results show that the deep brine in the middle of the basin has high salinity and is CaCl2 type water body. Based on the systematic analysis of the deep brine in the study area, it is found that the formation of the deep brine in the central part of the basin is related to the dissolution and filtration of rock salt and the strong metamorphism under the confined formation conditions. It is suggested that the B isotope was imported from Kunlun Mountain hot spring waters. The different sources of normal and trace elements reflect the “dual structure” characteristics of the material sources of deep brine. The results of this study will provide an important scientific basis for understanding the formation mechanism of deep brine in the whole Qaidam basin.