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The Qaidam Basin is a Mesozoic-Cenozoic compresso-shearing basin in western China. This basin has been subsiding since the Indosinian orogeny, and the subsidence is a strongly inherited feature in its Quaternary development. Five third-order sequences (SQ1, SQ2, SQ3, SQ4 and SQ5) were recognised using drilling/logging, coring and seismic data analysis. Each sequence was further divided into transgressive systems tract and regressive systems tract based on the maximum flooding surface. A sequence stratigraphic framework was established that revealed the distribution of sedimentary systems. Seven depositional systems, namely, alluvial fan, fan delta, braided-delta, shore lacustrine, shallow lacustrine, semi-deep lacustrine and incised valley depositional system, were identified from 105 well logs and 2D seismic lines covering 1600km. The sedimentary system distribution was identified as follows: (1) large-scale alluvial deposit located on the southern slope and adjacent to Kunlun Mountain and Yaber tectonic zone located northeast of the study area; (2) braided-delta deposits southeast of the Sanhu area; (3) widely developed fan-delta sediments on the base of Qigequan Formation in the Yaber tectonic zone; (4) well-deposited shoal lacustrine facies along the depositional strike in the regressive systems tract; (5) widely distributed shallow lacustrine facies; and (6) incised valley with large lateral extension and incision depth as an entity at the front of the Golmud Basin in the Sanhu area. Two different depositional models, namely, east and west models, were built by conducting an integrated analysis of sequence stratigraphy and sedimentary process. In the Sanhu area, the main controlling factors of the sequence architecture and depositional systems associations of the Qigequan Formation are tectonic subsidence and climate change with sediment supply and lake-level fluctuation secondary factors. This case study provides an example of the analyses of sequence stratigraphy and depositional systems in a salinised plateau basin. The approach combines seismic and sedimentary facies analysis to investigate Quaternary deposition and stratigraphy. The low-amplitude tectonic belt on the northern slope and the lithological traps on the southern slope are predicted to be favourable for the lithological gas reservoirs.