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.