Based on high resolution sequence stratigraphy theory, and according to the analysis of description of field outcrop profiles, cores, well drilling and logging trace, the Neogene upper Ganchaigou Formation in west segment,northern margin of Qaidam Basin are divided into two long-term base level cycles and six medium-term base level cycles. The deposition structure and stacking patterns of this two levels cycle are analyzed. Sequence stratigraphic framework of upper Ganchaigou Formation is established based on the sequence division of single well. The distribution feature of long-term base level cycle sequence has better relation with stratum. The long-term base level cycle sequence type of C2 mainly developed in the central basin and thick stratum areas, and the type of C1 mainly developed in the margin of the basin and thin stratum areas. Based on the sequence stratigraphic isochronous correlation framework, the lithofacies and paleogeographymap of the study area have been drawn up.