Three magnitude >6 earthquakes struck Qaidam, Qinghai province, China, in November 10th 2008, August 28th and 31st 2009 respectively. The Zongwulongshan fault has often been designated as the active seismogenic structure, although it is at odd with the data. Our continuous GPS station (CGPS), the Xiao Qaidam station, located in the north of the Qaidam basin, is less than 30 km to the southwest of the 2008 earthquake. This CGPS station recorded the near field co-seismic deformation. Here we analyzed the co-seismic dislocation based on the GPS time series and the rupture processes from focal mechanism for the three earthquakes. The aftershocks were relocated to constrain the spatial characteristics of the 2008 and 2009 Qaidam earthquakes. Field geological and geomorphological investigation and interpretation of satellite images show that the Xitieshan fault and Zongwulongshan fault were activated as left lateral thrust during the late Quaternary. Evidence of folding can also be identified. Integrated analyses based on our data and the regional tectonic environment show that the Xitieshan fault is the fault responsible for the 2008 Qaidam earthquake, which is a low dip angle thrust with left lateral strike slip. The Zongwulongshan fault is the seismogenic fault of the 2009 earthquakes, which is a south dipping back thrust of the northern marginal thrust system of the Qaidam basin. Folding takes a significant part of the deformation in the northern marginal thrust system of the Qaidam basin, dominating the contemporary structure style of the northern margin of the Qaidam basin and Qilianshan tectonic system. In this region, this fault and fold system dominates the earthquake activities with frequent small magnitude earthquakes.