Lanthanide-doped upconverting fluoride nano-and micro-materials have aroused much research interest due to their potential applications in phosphors, color displays, optical storages, solid-state lasers, solar cells and biomedical imaging. In order to synthesize Ln3+ doped crystals with favorable optical properties, such as high upconversion (UC) efficiency and controllable emission profile, the two major parameters that affect luminescence processes including host materials and lanthanide activator ions should be selected appropriately in the synthesis process. Majority of scientists deem that lanthanide doped fluoride nano-and micro-materials with low phonon energy are currently the efficient UC host materials. In this work, Yb3+ and Er3+ ions codoped NaYF4 and LiYF4 microcrystals are synthesized by a facile hydrothermal method with ethylene diamine tetraacetic acid (EDTA) as a chelator. The NaYF4:Yb3+/Er3+ and LiYF4:Yb3+/Er3+ microcrystals are characterized by X-ray diffraction (XRD), scanning electron microscope(SEM), and the photo-luminescence spectra method. The influences of EDTA on the crystal phase, shape and upconversion luminescence are explored in detail. According to the results of XRD and SEM, the pure hexagonal phased NaYF4:Yb3+/Er3+ rod-like microcrystals each with smooth surface are all around 12 m in the length. While the pure tetragonal phased LiYF4: Yb3+/Er3+ microcrystals each with smooth surface are octahedral in shape, and their average size is around 12 m. Under near infrared (NIR) 980 nm excitation, the two dominant emission peaks of Er3+ ions at 544 nm and at 650 nm are observed in NaYF4 and LiYF4 microcrystals, which can be assigned to the transitions of (2H11/2/4S3/2)4I15/2 and 4F9/24I15/2, respectively. It is found that the upconversion luminescence intensity of NaYF4:Yb3+/Er3+ microcrystals is about two times that of LiYF4:Yb3+/Er3+ microcrystals under the same excitation conditions. The ratio of red-to-green emission of Er3+ ions in LiYF4 microcrystals is higher than that of the NaYF4:Yb3+/Er3+microcrystals. The changes of the spectra in the different hosts could stem from two sources: one is that the nonradiation relaxation probability relative to phonon energy of matrix, the other is that the radiative transition probability relative to the site symmetry of the crystal field acting on the ion. The ratios between 5D07F1 and 5D07F2 transitions of Eu3+ ions in NaYF4:Yb3+/Eu3+ and LiYF4:Yb3+/Eu3+ microcrystals are employed to compare and elucidate the site symmetry of the crystal field for Ln3+ ions. Note that the ratio of 5D07F1 and 5D07F2 transitions in NaYF4:Yb3+/Eu3+ microcrystals is smaller than that of the LiYF4:Yb3+/Eu3+ microcrystals, which indicates a much higher radiative relaxation rate in NaYF4 microcrystals than in LiYF4 microcrystals. The organic ligands of EDTA on the surface of microparticles affect the properties of luminescence through changing the nonradiative relaxation rate, resulting in the different R/G ratios in NaYF4 and LiYF4 microcrystals. This result can be further supported by the comparison between NaYF4 and LiYF4 microcrystals without EDTA added in the preparation process. The micro-sized luminescence materials usually present stronger upconversion luminescence because of their higher degree of crystallinity and less surface quenching centers. Thus, the Er3+ codoped NaYF4 and LiYF4 microcrystals exhibit strong green upconversion emission, which has potential applications in full-color displays and microelectronic devices.