Hexagonal NaYF4 crystals with a variety of well-defined morphologies and sizes have been successfully synthesized through the precise manipulation of a series of experimental conditions, such as pH values and fluoride sources. X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) and photoluminescence spectra (PL) were used to characterize the final products. It is found that the intrinsic structure of NaYF4, the pH values and fluoride sources are responsible for the ultimate shape evolution of the final samples. The possible formation mechanism for β-NaYF4 samples with various morphologies has been proposed on the basis of XRD analysis and SEM investigation of the samples obtained at different reaction time periods. Additionally, the upconversion (UC) luminescence properties of Yb3+/Er3+ co-doped β-NaYF4 samples with different shapes have been systematically investigated and discussed. This study is expected to provide important information for morphology-controlled synthesis of other complex rare earth fluoride compounds.