—Results of profile magnetotelluric (MT) and magnetovariational (MV) soundings of the Pamir–Alai zone are presented. The problems of construction of a 2D geoelectric model of the lithosphere of the Pamir–Alai zone and its characteristics are considered. The results of the MT sounding inversion indicate the existence of a zone of lateral plastic flow in the Earth’s crust beneath the Alai depression, which manifested itself as a conductive lower-crust structure traced for at least 200 km in the E–W direction along the strike of the Alai depression. Analysis of the relationship between the parameters of the geoelectric structure and the seismicity distribution in the study region has revealed a spatial correlation between the location of the hypocenters of K > 11 earthquakes that occurred in the Pamir–Alai territory and the geoelectric structure of the Earth’s crust in this region. New data on the tectonic stratification of the Earth’s crust have been obtained, which permits us to supplement and refine the existing geological and geophysical data on the deep structure of the Pamir–Tien Shan junction zone. Conclusions about the nature of anomalous crustal conductivity in the Alai basin have been drawn.