In this article, hexagonal phase NaYF₄:Yb,Er (β-NaYF₄:Yb,Er) nanoparticles with a controlled size and morphology were synthesized via a simple and environmentally friendly method under relatively mild conditions. The different F⁻/Y³⁺ molar ratios were used in the synthesis of hexagonal Yb³⁺,Er³⁺ codoped NaYF₄ nanocrystals as a means of controlling the size and morphology of the nanocrystals. Subsequently, the morphology and structure of the products were characterized by transmission electron microscopy (TEM) and X-ray diffraction (XRD). The effect of the F⁻/Y³⁺ molar ratio on the size and morphology of the products was examined. When the F⁻/Y³⁺ molar ratio was gradually increased, the products transformed from spherical hexagonal nanocrystals to regular hexagonal nanocrystals and the size of the products changed from 8 to 400 nm. That is to say, excessive F⁻ ions were capable of accelerating for the formation of larger β-NaYF₄:Yb,Er nanoparticles in our synthesis procedure. Meanwhile the upconversion photoluminescence of the nanocrystals was investigated in detail by fluorescent spectroscopy to reveal the relationship between the optical properties and the morphology and size of the products. As a consequence, the upconversion photoluminescence of the nanocrystals demonstrated a morphology and size dependence. Thus the fabrication of β-NaYF₄:Yb,Er nanoparticles with different sizes and morphologies would satisfy the diverse requirements in various fields.