The current stress state of the Earth's crust in Central Asia depends entirely on the interaction of the Eurasian plate with the Indian and Arabian plates. Moreover, an essential role in this action is played by the subduction process in the Pamir-Hind Kush zone. In this region, deep earthquakes and anomalies in seismic velocities indicate subduction of the Indian Plate. To determine the effect of earthquakes on the stress state of the Earth's crust in Central Asia, we analyzed the hypocenters according to the available data over a hundred years. Taking the envelope of the hypocenters as the surface of the subducted indenter, we analyzed its penetration into the mantle. Instead of the pushing force of the indenter, the velocity of the Indian plate is taken into consideration. A model of the stresses is constructed on the equations of creeping motion of a viscous incompressible fluid. The stress variation in the Earth's crust and mantle was calculated as the stress difference before and after the earthquake. The mechanism of earthquakes is modelled by an introduction of equivalent volume forces in the equilibrium equations corresponding to a couple dipoles without a moment. The equations of creeping motion are numerically solved using boundary element methods. Numerical experiments with different physical model parameters for the Earth's crust and mantle were conducted. To introduce the negative buoyancy of the subducting plate, partial eclogitization of the rocks in the collision zone was assumed. As a result, a certain combination of stiffness and density was determined for the lithosphere and mantle, which explained the peculiarities of this region. The influence of crustal and mantle earthquakes in the Pamir-Hindu Kush region on the change in background stresses in Central Asia was analyzed which are not higher than 2–3%.