Structural and electronic properties of ultrathin nanocrystals of chalcogenide Bi2(Tex Se1-x)3 were studied. The nanocrystals were formed from the parent compound Bi2Te2Se on as-grown and thermally oxidized Si(100) substrates using Ar-assisted physical vapor deposition, resulting in well-faceted single crystals several quintuple layers thick and a few hundreds nanometers large. The chemical composition and structure of the nanocrystals were analyzed by energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, electron backscattering, and X-ray diffraction. The electron transport through nanocrystals connected to superconducting Nb electrodes demonstrated Josephson behavior, with the predominance of the topological channels [Stolyarov et al. Commun. Mater., 2020, 1, 38]. The present paper focuses on the effect of the growth conditions on the morphology, structural, and electronic properties of nanocrystals.