The eastern margin of the Qaidam Basin lies in the key tectonic location connecting the Qinling, Qilian and East Kunlun orogens. The paper presents an investigation and analysis of the geologic structures of the area and LA-ICP MS zircon U-Pb dating of Paleozoic and Mesozoic magmatisms of granitoids in the basement of the eastern Qaidam Basin on the basis of 16 granitoid samples collected from the South Qilian Mountains, the Qaidam Basin basement and the East Kunlun Mountains. According to the results in this paper, the basement of the basin, from the northern margin of the Qaidam Basin to the East Kunlun Mountains, has experienced at least three periods of intrusive activities of granitoids since the Early Paleozoic, i.e. the magmatisms occurring in the Late Cambrian (493.1±4.9 Ma), the Silurian (422.9±8.0 Ma-420.4±4.6 Ma) and the Late Permian-Middle Triassic (257.8±4.0 Ma-228.8±1.5 Ma), respectively. Among them, the Late Permian - Middle Triassic granitoids form the main components of the basement of the basin. The statistics of dated zircons in this paper shows the intrusive magmatic activities in the basement of the basin have three peak ages of 244 Ma (main), 418 Ma, and 493 Ma respectively. The dating results reveal that the Early Paleozoic magmatism of granitoids mainly occurred on the northern margin of the Qaidam Basin and the southern margin of the Qilian Mountains, with only weak indications in the East Kunlun Mountains. However, the distribution of Permo-Triassic (P-T) granitoids occupied across the whole basement of the eastern Qaidam Basin from the southern margin of the Qilian Mountains to the East Kunlun Mountains. An integrated analysis of the age distribution of P-T granitoids in the Qaidam Basin and its surrounding mountains shows that the earliest P-T magmatism (293.6-270 Ma) occurred in the northwestern part of the basin and expanded eastwards and southwards, resulting in the P-T intrusive magmatism that ran through the whole basin basement. As the Cenozoic basement thrust system developed in the eastern Qaidam Basin, the nearly N-S-trending shortening and deformation in the basement of the basin tended to intensify from west to east, which went contrary to the distribution trend of N-S-trending shortening and deformation in the Cenozoic cover of the basin, reflecting that there was a transformation of shortening and thickening of Cenozoic crust between the eastern and western parts of the Qaidam Basin, i.e., the crustal shortening of eastern Qaidam was dominated by the basement deformation (triggered at the middle and lower crust), whereas that of western Qaidam was mainly by folding and thrusting of the sedimentary cover (the upper crust).