Theoretical study of thermodynamic stability of compact three-dimensional heterostructure film nanochips GaAs/GaAs_xN_y/GaN has been performed by computer simulation. The paper presents a three-stage scheme of computer simulation which includes three successive stages: creation of topological-geometrical model of nanochips, their structural relaxation and Helmholtz free energy calculation of relaxed nanochips. Thermodynamic stability of hexagonal or cubic crystal structures of GaN nano layer in nanochip GaAs/GaAs_xN_y/GaN has been determined by the criterion of minimum of relaxed nanochips Helmholtz free energy. The study has been conducted in the temperature range from 500 to 900 °C for film nanochips GaAs/GaAs_xN_y/GaN formed on the GaAs crystal surface of (111) and (100) orientation. It has been shown that stable thermodynamic state of a GaN nanolayer is observed at zero concentration of nitrogen atoms in the superficial layer of GaAs. This is equal to the absence of the transition layer in nanochips heterostructure. On the subsrate GaAs (100) the formation of GaN layer in hexagonal structure is thermodynamically preferable, whereas in cubic structure GaN layer is more stable on the substrate GaAs (111). Concentration ranges of the nitrogen atoms in the intermediate layer GaAs_xN_y have been defined. They ensure metastable state of cubic or hexagonal structure of gallium nitride nanolayer on GaAs (100) and GaAs (111) substrates.