Pure hexagonal NaYF₄:Yb³⁺,Ln³⁺ (Ln³⁺ = Er³⁺, Tm³⁺, Ho³⁺) crystals were obtained for the first time through a facile microwave (MW) reflux method at relatively low temperature (160 °C) and atmospheric pressure within only 50 min. By controllably increasing the NH₄F content in the ethylene glycol (EG) solvent, the phase of as-prepared NaYF₄:Yb³⁺,Ln³⁺ gradually transforms from cubic to hexagonal. Correspondingly, the up-conversion (UC) emission intensities of hexagonal NaYF₄:Yb³⁺,Ln³⁺ (Ln³⁺ = Er³⁺, Tm³⁺, Ho³⁺) are increased by 10–12 times compared to those of the cubic phase. A possible growth mechanism for the phase transformation under these MW conditions has been proposed. Moreover, for the first time, we introduced Bi³⁺ ion into β-NaYF₄:20%Yb³⁺,2%Ln³⁺ crystals. As expected, the UC emission of β-NaYF₄:Yb³⁺,Ln³⁺,Bi³⁺ are about 10–40 times higher than those of Bi³⁺ free samples. It is found that tri-doping of Bi³⁺ doesn't change the basic emission of Ln³⁺ ions. XRD results gives evidence that tri-doping of Bi³⁺ ions can tailor the local crystal field and dissociate the Yb³⁺ and Ln³⁺ ion clusters, which is the main reason for the UC enhancement. This designed MW reflux method for the synthesis of β-NaYF₄:20%Yb³⁺,2%Ln³⁺ can be applied to prepare other rare earth fluorides. The markedly enhanced UC luminescence through Bi³⁺ doping also provides an effective way to gain very bright UC emission.