Theoretical multiscale model of nitride semiconductor nanostructure is proposed. The model combines various computational methods such as density functional theory, molecular dynamics and kinetic Monte Carlo. As a first step of implementation of proposed approach ab initio calculations of structural and electronic properties of two different structures InN/Si and AlN/AlGaN/GaN heterostructures were carried out. In particular, the influence of oxygen on InN/Si adhesion energy was studied. AlN, GaN, AlxGa1-xN (x=0.33) spontaneous and piezoelectric polarizations as well as sheet carrier concentrations at GaN/AlGaN interface were calculated. Obtained value for sheet carrier concentration at GaN/AlGaN interface is close to experimental data.