Lithium possesses exceptionally high economic and strategic significance. China’s lithium resources rank second globally, predominantly found in salt lake brine. Recently, clay-type lithium deposits have been discovered in the Mahai Salt Lake within the Qaidam Basin, featuring a broad distribution area, stable production layers, and thick strata. This paper investigates the mineral sources and mining circumstances of the clay deposits in the study area through the principal trace elements and Sr and Li isotopes of the clay rocks. The study reveals that the sedimentation of the clay deposits in the study area is mainly semi-brine–brackish water phase sedimentation, formed in a shallow water environment of weak oxidation. A terrigenous source characterizes the clay sediment. The tectonic setting of the study area shares common traits with a continental island arc-active continental margin, and the abundant lithium clay rocks mainly receive contributions of feldspar, amphibole, pyroxene, etc. The primary sediment source of the clay deposits mainly stems from igneous and quartz sediment source areas. The 87Sr/86Sr value indicates that the Sr source of the clay rocks in the study area is the shallow over-pressured brine and Yuka River water, mainly derived from the weathering dissolution of silicate rocks. The δ7Li value indicates that the lithium in the lithium-rich clay rocks mainly originates from the release of lithium from silicate minerals in the surrounding mountain ranges, carried by Yuka River water, and from the supply of lithium from the deep Ca-Cl type water body. The research findings establish a foundation for the future exploration and development of clay-type lithium deposits in salt lake regions.