Located at the northeastern margin of the Qinghai-Tibet Plateau (QTP) in the Asian interior, the Lake Qinghai is sensitive to environmental change and thus an outstanding site for studying paleoenvironmental changes. Thick deposits in the Lake Qinghai provide important geological archives for obtaining high-resolution records of continental environmental history. The longest drilling core obtained from the Lake Qinghai, named Erlangjian (ELJ), reached about 1109 m and was investigated to determine its clay mineral assemblage and grain size distributions. Clay mineralogical proxies, including type, composition, and their ratios, as well as the illite crystallinity (KI) and chemical index (CI), in combination with grain size data, were used for reconstructing the history of paleoenvironmental evolution since the late Miocene in the Lake Qinghai Basin. The clay mineral records indicate that the clay mainly comprise detritus originating from peripheral material and has experienced little or no diagenesis. The proportion of authigenic origin was minor. Illite was the most abundant clay mineral, followed by chlorite, kaolinite, and smectite. Variations of clay mineral indexes reflect the cooling and drying trends in the Lake Qinghai region, and the grain size distribution is coincided with the clay minerals indexes. The paleoclimatic evolution of the Lake Qinghai Basin since the late Miocene can be divided into five intervals. The climate was relatively warm and wet in the early of late Miocene, then long-term trends in climate change character display cooling and drying; later in the late Miocene until early Pliocene the climate was in a short relatively warm and humid period; since then the climate was relatively colder and drier. These results also suggest multiple tectonic uplift events in the northeastern QTP.