A M_W6.4(M_S7.0)earthquake occurred in Gonghe, Qinghai on 26 April 1990. The Gonghe area is located on the northeastern margin of the Qinghai-Tibet Plateau. The geological tectonic movement in this area is mainly affected by the uplift of the Qinghai-Tibet Plateau. There has been no earthquakes larger than moderate strength in the Gonghe Basin since the historical records, and there are no large-scale active faults on the surface of the epicenter area, so the earthquake has aroused great concern. No major earthquakes have occurred in the Gonghe area since 1995, but the data of small earthquakes is very rich, which ensures the completion of the research. The TomoDD method combines the double-difference relocation method with seismic tomography, and solves two problems at the same time, one is the problem of fine positioning of the earthquake, and the other is the calculation of the 3D velocity structure of the earth’s crust. In this paper, we collected 63872 P and S wave arrival time data in Gonghe and surrounding area recorded by Qinghai, Gansu seismic networks and temporary seismic array from January 2009 to January 2019. The 3D crustal velocity structure and source position parameters of the region are inversed. The relationship between the geological structure setting of the main shock and the velocity structure and seismicity of the region was analyzed. The results show that the crustal velocity structure in the Gonghe area shows lateral inhomogeneity. The Gonghe mainshock is located in the low-velocity anomaly directly below the Gonghe Basin, close to the high-low-velocity anomaly boundary. There is an obvious high-speed anomaly in the southwest of the mainshock, which thrusts from underground to near-surface in the northeast direction. It is estimated that the Wayuxiang-Lagan concealed fault is located at 35.95°N, the dip of the fault is about 45° at the deep part. It is inferred that the occurrence of the Gonghe main shock is caused by the sliding of the Wayuxiangka-Lagan Fault whose strike is NWW and dip is SSW under the action of horizontal tectonic stress. The high-velocity anomaly is about 5~40km deep underground in the northeast direction of the Riyueshan Fault, and a large number of small earthquakes occurred around the high- and low-velocity transition zone. It is presumed that under the action of the near-horizontal NE-directed tectonic stress, the high- and low-velocity zones were further interacted to generate faults and ground folds, and a large number of small earthquakes occurred during the fusion process.