Through analysis and inversion of the aeromagnetic anomaly field, this paper has studied the magnetic basement of the Junggar basin. The separation of anomalies is the pre-requisite of the inversion- The regional magnetic field in the basin varies considerably and almost covers all other types of anomalies. The bottom of the magnetic crust estimated by the extreme points of power spectra is close to that estimated by the matrix spectrum method in depth, and this convincingly provides evidence for the determination of the regional field. Using the matrix spectrum method with the help of forward simulation, one can understand the local buried depth of the basement and obtain the basis which might be regarded as homogeneous magnetization so as to make inversion with Hahn's method. The relief of the magnetic basement of the basin shown by the inversion is quite consistent with the near-surface great fault. It is revealed that, due to the influence of the shape of the basin, faulting was dominant under the action of the north-south compressive stress and, as a result, this basement was divided into three tectonic units by a fork-shaped uplifted zone. The above studies combined with the geological, remote sensing and gravitational data analysis show that the basement is characterized by strong magnetism, high density and u ifrom physical property, belonging to the rigid old crystalline basement. Controlled by the basement, the basin not only remained stable in the upper part for a long period, but played the role of main tectonic stay in the geological evolution of Northern Xinjiang.