Abstract: In this work, the results of studying the microstructure and superconducting properties of ultrathin films on the basis of NbN in the initial state and after modification by being subjecting to composite ion beam irradiation with the energy ~1–3) keV are presented. HRTEM analysis showed that the initial films on the sapphire substrate in orientation “c-cut” are characterized by a grain size essentially exceeding the film thickness, while on the other substrates the size of grains corresponds to the thickness of film. Using XPS analysis, it was shown that in the initial films the atomic ratio of Nb and N is 0.51/0.49, respectively, the percentage of oxygen being lower than 5%. For ultrathin films 5 nm in thickness, the critical temperature of transit to superconducting state (T c) is found to be ~3.6 K and the density of critical current is jc ~8MA/cm2. In the work it is experimentally determined that the irradiation of NbN films by composite ion beams leads to the controlled modification of its superconducting properties due to the process of selective substitution of nitrogen atoms on the oxygen atoms.