At 06:34 CST on November 18, 2017, an M s6.9 earthquake struck Mainling prefecture, Nyingchi City, Tibet. The earthquake occurred at the frontier zone of collision and subduction in the eastern Himalayan syntaxis, a region of persistently strong compression between India and Eurasia. To monitor aftershock activity, the Institute of Tibetan Plateau Research, Chinese Academy of Sciences, installed 28 broadband seismic stations around the epicentral area and obtained 180 days of seismic observation data. The average spacing between stations was approximately 5 km, which yielded good coverage of the source area and enriched the seismic data for the Eastern Himalayan syntaxis. In this paper, the hypodense events are refined by the hypoDD double-difference seismic location method and the local tomography software (LOTOS-12), an algorithm for seismic location and velocity structure imaging joint inversion. The hypoDD seismic localization method uses waveform cross-correlation technology to achieve positioning using the minimum residuals of the actual and theoretical travel times of two earthquakes. It is widely used for close-range earthquakes and is suitable for regional earthquake research; the LOTOS algorithm is more appropriate for velocity structure inversion in regions with significant differences in physical properties. The results show that the aftershock zone is approximately 50 km long and 30 km wide and trends NW-SE. According to the aftershock distribution, three active faults are basically consistent with the strike of the Xixingla fault zone. These active fractures are similar in shape and have a NE dip direction, and the dip angles of the active faults gradually become steeper from NW to SE. Under the continuous NE thrusting action of the Namche Barwa syntaxis, the three secondary fractures have undergone bending deformation. This deformation is associated with the adjustment mode of the eastern Himalayan syntaxis where the Indian plate continues to push Eurasia northward. At the same time, combining these results with those of the LOTOS-12 algorithm, the distribution of the Pg wave and Sg wave velocity disturbance in the shallow crust (20 km) and the wave speed ratio ( V p/ V s) are obtained. The main shock was located in an abnormal transition zone of body wave velocity, and the aftershocks mostly occurred in the negative anomaly zone for P wave and S wave velocities, which reflects the characteristics of stratigraphic fractures and faults in the area with concentrated earthquakes. We suggest that this area should be avoided in the future when construction of engineering facilities is required north of Namche Barwa Peak. Overall, with Namche Barwa Peak as the boundary, the P wave and the S wave are generally characterized by high-speed anomalies in the north and low-speed anomalies in the south. This phenomenon may be related to the geological structure and petrophysical properties in this area, as the lithologies of the Lhasa terrane are old and cold; meanwhile, the metamorphic body in the south and the Namche Barwa syntaxis are relatively broken, the ages of rock formation are relatively young, and the lithologies are relatively hot and soft. In addition, high-speed P wave anomalies in the northwestern part of Namche Barwa Peak may be related to enrichment in garnet minerals in this area. The higher wave velocity ratio on the southwest side of the epicentral area, the lower P wave velocity on the right side of profile 1–1′ and the P wave on the left side of profile 2–2′ may be related to the fragmentation of the terrain in this area and the development of valley glaciers. The area where the wave velocity ratio is relatively large may also be related to the upwelling of asthenospheric and lithospheric material in the deep mantle.