The theory of quantum relaxation of nanoelectromechanical systems (NEMS) energy storage in materials is under consideration. By using the method of quantum kinetics the relaxation of NEMS energy storage in the form of Fe₁₇₂ сuboid limited by (100) type planes in fcc iron crystal has been studied. For comparison, the calculation of a similar structure atomic Fe₁₇₂ cluster has been carried out by molecular dynamics (MD) method for the temperature T = 293 K. The analysis of computer- related experiments has shown that the relaxation of the NEMS energy storage of Fe₁₇₂ and Fe₁₇₂ MD atomic cluster from initial nonequilibrium state has significant differences both in kinetics, and in the variety of structural transformations. It is shown that iron MD cluster relaxation is insignificant and its final total binding energy per atom is 2 eV/at lower than the crystal one. NK method has revealed that under relaxation there is a significant change in the shape and the pair radial distribution function of NEMS energy storage nuclei. It significantly increases binding energy up to 3,34 eV/at, which is only about 1 eV/at less than the binding energy of crystalline iron. The opportunity of self-organization NEMS energy storage process through several intermediate metastable states has been shown. It is manifested that fluctuation rebuild of cube into cuboid with strong bending of cube surfaces occurs at the 20 ps of relaxation, and there is the second transformation with trapezoid change of faces at the 40 ps of relaxation process. This effect cardinally differentiates NK relaxation of the NEMS energy storage cuboid Fe₁₇₂ from MD relaxation of atomic Fe₁₇₂ clusters in crystalline iron.