A comprehensive characterization of NaYF₄ nanocrystals synthesized in trioctylphosphine oxide has been reported in order to present an effective method of monodisperse, small, hexagonal nanocrystal synthesis in a high boiling organic solvent via a co-thermolysis pathway. We observed the influence of temperature, Na/Y precursors ratio and time of the synthesis on the nanocrystals size, shape and crystal structure. For that purpose, we characterized the structure of as-synthesized nanocrystals by X-ray diffraction and transmission electron microscopy. Moreover, all nanocrystals were doped with Eu³⁺ ions, which were used as an optical crystal field probe. We applied photoluminescence, PL excitation and absorbance spectra to determine the influence of crystal symmetry, surface to volume ratio and ligands on the optical properties of doped Eu³⁺ ions. It was found that trioctylphosphine oxide reduces the free-energy barrier and stimulates the NaYF₄ crystallization in the hexagonal phase, even at relatively low temperature. A similar effect was observed when the excess of sodium trifluoroacetate precursors was used. Moreover, the presented nanocrystal evolution within synthesis time confirmed that at suitable conditions NaYF₄ crystallized in the hexagonal phase within less than 5 min. Optical spectroscopy investigations confirmed the high quality of small β-NaYF₄:Eu³⁺ nanocrystals, which are promising candidates for e.g. optical markers in the visible wavelength range.