Upconversion emission intensity and morphology are both important features of NaYF4:Yb3+, Er3+ microcrystals. In this paper, myristic acid (MA) is selected as a novel stabilizing ligand to synthesize NaYF4:Yb3+, Er3+ through a facile hydrothermal method. Upconversion fluorescence spectra indicate that the emission intensity of product prepared with MA as ligand has increased dramatically compared with the sample prepared using commonly used oleic acid (OA) as ligand. Field emission scanning electron microscopy (FE‐SEM) results display that the morphology of NaYF4:Yb3+, Er3+ obtained using MA as ligand can be tuned from nanodisk, nanorod to nanotube. Especially, nanotube with clear caves can be prepared directly with proper concentration of base (NaOH). And powder X‐ray diffraction (XRD) analysis reveals a relationship between the phase transformation process and the amount of NaOH. With increasing the amount of NaOH, the transition process of cubic phase to hexagonal phase is accelerated. The effect of F− and OH− on the fluorescence properties of NaYF4:Yb3+, Er3+ are studied systematically. A gradual increase of the amount of NaF results in a regular increase of the emission intensity. On the contrary, the emission intensity decreases with increasing the amount of NaOH. In addition, reasonable explanations of the influence of F− and OH− on emission intensity are given as well.