Highly uniform, monodisperse, luminescent and mesoporous hexagonal NaYF4 microspheres were successfully prepared at low temperature (down to 80 °C) by a facile one-step polyol-mediated solvothermal route in the presence of trisodium citrate. The crystalline structure, size, morphology, phase transition and luminescence properties were studied. Surfactant of citrate anions (Cit3−) was found to induce a self-assembly process in the ethylene glycol system, which plays an important role in forming the mesoporous microspheres and promoting the cubic to hexagonal phase transition by increasing system-free energy and decreasing energy barrier of phase transition. These mesoporous β-NaYF4 microspheres have expected up-conversion luminescence by codoping of Yb/Er upon infrared excitation. The existence of mesoporous structure and up-conversion luminescence enable these microspheres have potential in biological applications.