We develop an essentially nonlinear theory of elastic and nonelastic microstrains resulting in the formation of nanostructures. Using the model of mutually penetrating lattices, we generalize the well-known theory of acoustic and optical vibrations to the case of nonlinear interaction between sublattices. This permits treating the sublattice interaction forces as periodic ( for example, sinusoidal) functions of the relative displacement of the sublattices. We obtain equations for the macroscopic and microscopic displacement fields containing two characteristic scales of the nanostructure. We find a number of their solutions describing the effects of decrease in the potential interatomic barriers in the external stress field and the formation of defects and domain nanostructure as a result of bifurcation transitions. We prove their stability.