The nanostructure and the phase stability on the 17 nm and the 2 nm epitaxial ZrO2 thin films grow on p-Si(001) wafers have been considered. Wide angle X-ray reciprocal space mapping and high resolution transmission electron microscope (HRTEM) analysis have shown that many ferroelastic 90° and 180° domains, of which 001 plane align nearly in out-of plane direction for 17nm ZrO2 thin films with large roughness. 2 nm ZrO2 ultra-thin film has shown that nm sized precipitates exist in the matrix. Diffractograms from the plan-view image indicate that the matrix is tetragonal phase and that the precipitate is monoclinic one. The monoclinic phase has the coherent interface between tetragonal matrixes without misfit dislocation. The aberration-corrected HRTEM image clearly shows O atoms as light gray spots as well as Zr atoms as dark gray spots, which elucidates the existence of the structural transition layer between the tetragonal and the monoclinic phases. This result indicates that the transition layer would relax the large strain due to the martensitic phase transition. The ultra-thin film is estimated to be under compressive stress state from the lattice images of both of the phase, which controls the nucleation of the monoclinic phase.