Data for the vapor-phase doping (300°C) of nickel phthalocyanine (NiPc) by sodium taken in different concentrations (x), as well as structural analysis data for Na x = 0.2 NiPc, Na x = 1 NiPc, and Na x = 3 NiPc samples, have been reported. The structure of the samples and their atomic configuration versus the doping level have been studied by transmission electron microscopy, Raman scattering, X-ray diffraction, X-ray absorption spectroscopy, and extended X-ray absorption fine structure (EXAFS) spectroscopy. The structural parameters of Ni-N, Ni-C, and Ni-Ni bonds have been determined, and it has been found that, at a low level of doping by sodium, local structural distortions are observed in some molecules of the NiPc matrix near nickel atoms. The fraction of these molecules grows as the doping level rises from x = 0.2 to x = 1.0. It has been shown that doping changes the oscillation mode of light atoms, which indicates a rise in the electron concentration on five-and six-membered rings. At a high level of sodium doping (x = 3.0), nickel nanoparticles with a mean size of 20 nm and molecule decomposition products have been observed in the NiPc matrix. It has been found that the fraction of nickel atoms in the Na x = 3 NiPc nanoparticles as estimated from EXAFS data is sufficient for the room-temperature magnetic properties of the samples to persist for a long time.