Nanocrystalline (Y,Gd)BO₃∶Eu with different particle sizes have been prepared by the thermal decomposition of precursors that contain rare earths–EDTA and H₃BO₃–EDTA complexes (EDTA = ethylenediaminetetraacetic acid). The effects of synthesis temperature, [Y]/[Gd] value, and doping concentration of Eu³⁺ ions on the crystallization and luminescent characteristics of the (Y,Gd)BO₃∶Eu nanocrystals were investigated. The materials began to crystallize at 700 °C in air or 650 °C in oxygen with a hexagonal vaterite-type structure, except that a small amount of triclinic phase was seen at a low [Y]/[Gd] value. By increasing the [Y]/[Gd] value and the calcination temperature, the triclinic phase could be eliminated. XRD patterns indicated that (Y,Gd)BO₃∶Eu nanocrystals with smaller particle size possessed a more distorted lattice, which could be responsible for the size-dependent color purity evidently showed in their photoluminescence spectra, as the ratio of the red emission (⁵D₀ → ⁷F₂) to the orange emission (⁵D₀ → ⁷F₁) (R/O) was much higher in the smaller particles. The Eu³⁺ quenching concentration and the optimum Gd³⁺ substitution also exhibited the size-dependent characteristics. Their possible mechanisms were proposed.