<p>In-depth study of the shallow structure of active tectonic has important guiding significance for analyzing its strong earthquake deformation characteristics, major project site selection and avoidance distance. In this paper, we are used to investigation the Miaoergou-Bamudun area in the eastern of the Hami Basin Northern Margin Fault (HMNF) by two geophysical methods, audio magnetotelluric and micro-motion. The detection results reveal the shallow structure of the HMNF. Audio magnetotelluric and micro-motion detection results show that the fault width of the HMNF is about 30–90 m, which has the characteristics of ‘steep dip angle, obvious difference in electrical and shear wave velocity and broken bedrock’. The local section shows that the HMNF obviously thrusts offset the bedrock and overlying the Quaternary colluvial or alluvial gravel caprock. The thrust offset is about 50–90 m, and obvious scarps are formed on the surface. Based on the comprehensive analysis of the shallow structure of the HMNF revealed by the audio magnetotelluric and micro-motion profiles, the width of the possible strong earthquake deformation zone caused by the HMNF is preliminarily evaluated. The slip rates of the HMNF in different sections have a pattern of alternating strong and weak distribution. Combined with the shallow structure of the HMNF, it is considered that the main deformation in the eastern Tianshan area is that the compression thrust deformation of the piedmont thrust faults controls the uplift of the mountain rather than the shortening deformation.</p>