The saline lacustrine hybrid sedimentary rocks are complex in lithology and unknown for their sedimentary mechanisms. The hybrid sedimentary rocks samples from the Neogene upper Ganchaigou Formation to lower Youshashan Formation (N1–N21) in the Fengxi area Qaidam Basin, were investigated through core-log and petrology-geochemistry cross-analysis by using the core, casting thin section, scanning electron microscope, X-ray diffraction, logging, and carbon/oxygen isotopic data. The hybrid sedimentary rocks in the Fengxi area, including terrigenous clastic rock and lacustrine carbonate rock, were deposited in a shallow lake environment far from the source, or occasionally in a semi-deep lake environment, with 5 lithofacies types and 6 microfacies types recognized. Stable carbon and oxygen isotopic compositions reveal that the formation of sedimentary cycles is controlled by a climate-driven compensation-undercompensation cyclic mechanism. A sedimentary cycle model of hybrid sedimentary rocks in an arid and saline setting is proposed. According to this model, in the compensation period, the lake level rises sharply, and microfacies such as mud flat, sand-mud flat and beach are developed, with physical subsidence as the dominant sedimentary mechanism; in the undercompensation period, the lake level falls slowly, and microfacies such as lime-mud flat, lime-dolomite flat and algal mound/mat are developed, with chemical-biological process as the dominant sedimentary mechanism. In the saline lacustrine sedimentary system, lacustrine carbonate rock is mainly formed along with regression, the facies change is not interpreted by the accommodation believed traditionally, but controlled by the temporary fluctuation of lake water chemistry caused by climate change. The research results update the interpreted high-resolution sequence model and genesis of hybrid sedimentary rocks in the saline lacustrine basin and provide a valuable guidance for exploring unconventional hydrocarbons of saline lacustrine facies.