The origins and formation mechanisms of neotectonic structures in a part of the Mongolian-Siberian region were identified by geodynamic zoning based on multidimensional statistical analysis of numerical arrays describing geological-geophysical and geological-geomorphological processes. These processes in the regional lithosphere were described by a set of 11 geological and geophysical parameters, divided into three main groups using the hierarchical method of cluster analysis. The first group includes the seismic moment, the density of active faults, the rates of current horizontal deformations, and the magnitude of the deep heat flow. The second group involves the thicknesses of the earth’s crust and exogenous active layer, the velocities of current horizontal movements, and the amplitudes of vertical neotectonic movements. The third group includes gravity anomalies and the lithosphere thickness. The spatial grouping of parameters by cluster analysis (K-means method) yields seven clusters, whose spatial position and composition are determined by the geological history, geological structure, geodynamic evolution of the region, and the current deformation rates. Some clusters characterize large rigid lithospheric blocks, while other clusters describe large active fault systems in the given area. The search for latent factors that make the greatest contribution to the dispersion of the geological and geophysical parameter values was carried out using the principal component method, which makes it possible to minimize the number of factors. Four main factors were identified for areas that differ in the morphology and origin of neotectonic structures: (i) higher horizontal compressive and tensile strains, (ii) dynamic effect of mantle anomalies, manifested in uplifts and arching, (iii) activation of thinned lithosphere within the boundaries of lithospheric plates and large blocks, and (iv) active shear deformation of the earth’s crust. The results of clustering and factor analysis of numerical arrays describing the geological-geophysical and geological-geomorphological processes within the Mongolian-Siberian region can be interpreted in the framework of physical mesomechanics.