Since Singer (1984) reviewed clay minerals as they relate to paleoclimates, clay minerals have been used to reconstruct paleoclimates and environments. However, the paleoclimate information recorded by the paleo-clays in sediments will be overprinted or changed if the clay minerals undergo diagenetic transformations or post-depositional diagenetic changes, which are quite common. However, numerous studies still use clay minerals to reconstruct paleoclimates and paleo-environments. Uplift of the Tibetan Plateau since the Late Miocene has significantly impacted the sediments of the Qaidam Basin. However, due to the scarcity of fully dated sediment records, we know little about whether or not and/or how these clay minerals responded to this uplift. In order to understand their response to the uplift, in this study, we present the results of high-resolution profiling of the clay minerals from a 938.5-m borehole core (SG-1) from the Qaidam Basin (NE Tibetan Plateau). These clay minerals are mainly composed of illite, mixed layers of illite/smectite (I/Sm) and chlorite, with minor kaolinite and smectite. The clay minerals may have undergone early diagenesis. The delta O-18-delta D values of the interlayer water and the clay minerals imply the following. (a) The primary amounts of illite and chlorite were lower than those observed, while the primary amounts of smectite and kaolinite were higher than those observed; the amounts of clay minerals should be careful to be used to reconstruct paleo-environment singly; the changes in the illite "crystallinity" (Kubler Index) and chlorite "crystallinity" (Arkai Index) were related to changes in salinity and temperature. (b) Chemical weathering from 2.77 to 0.1 Ma was stronger than that at present. (c) The delta O-18 and delta D of the interlayer water ranged from -11.8 to 82.95%o and from -114.3 to 165.5%o, respectively, which was related to pore water and/or lake water undergoing strong evaporation. The isotopic composition of the interlayer water reflects variations in the pore water/lake water or of the reacting solutions, and records changes in environment. (d) The clay minerals recorded climate changes and uplift in the core, with a dramatic shift at 1.2 Ma and two different environment stages at 2.77-1.2 Ma and 1.2-0.1 Ma.