Hexagonal sodium yttrium fluoride crystals with predictable shapes, such as microtubes, microspheres, microrods, micro-bipyramids, microplates, and microprisms, have been synthesized by simply tuning the molar ratio of NaF to RE3+ (RE represents the total amount of Y3+ and the doped rare earth elements such as Yb3+, Er3+). The structural and kinetic factors that govern the phase and shape evolution of NaYF4 crystals have been carefully studied, and the influence of NaF to RE3+ ratio on phase and morphology evolution was systematically investigated and discussed. It is found that the molar ratio of NaF to RE3+ can strongly control the size and structure of as-prepared β-NaYF4 : Yb3+/Er3+ samples owing to the difference of capping effect of F− on the different crystal planes of β-NaYF4 microcrystals. By choosing bipyramidal β-NaYF4 microdisks as a candidate, the possible formation mechanism was proposed on the basis of XRD analysis and SEM observation of the products at the different reaction time periods. Most interestingly, the upconversion (UC) luminescent properties of β-NaYF4 crystals show that the optical properties of as-synthesized materials with different morphologies exhibit great distinction. This study is expected to be suggestive for the precisely controlled growth of other complex rare earth fluoride compounds and provide a reference for exploration of the morphology-dependent UC luminescence properties.