In a hydrothermal atmosphere with high temperature and long reaction time, a kind of special rare earth doped fluoride microcrystal was obtained with Sc3+ co-doping. The crystal phase and morphology of as-prepared samples were characterized with X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray detector (EDX) and element mapping. It is found that the Sc3+-free sample can be ascribed to the pure hexagonal NaGdF4, and the Sc3+-doped samples are composed of hexagonal NaGdF4- and monoclinic Na3ScF6-based microcrystals. With increasing of the doped concentration of Sc3+, the morphology of NaGdF4-based microcrystal changes from lantern with cracked ends to octadecahedron with smooth surfaces, accomplished with a decreased size. It is worth mentioning that the concentration of Sc3+ that really entered into the host lattice is much less than the Sc3+ concentration in the precursor. Excited by 980 nm laser, the upconversion emission spectrum of single microcrystal was obtained by laser scanning confocal microscopy technology. For a single NaGdF4∶Yb3+,Er3+ microcrystal, the significant upconversion fluorescence regulation was obtained by doping a few Sc3+ into the host lattice, and the relative intensity of the green upconversion emission (2H11/2/4S3/2→4I15/2) to the red counterpart (4F9/2→4I15/2) increases gradually with the increasing of Sc3+ doped concentration. Combining with the suggested upconversion mechanisms, the influence of Sc3+ doped concentration on the rise time of upconverion fluorescence decay curve and the dependence of integrated intensity of upconverion emission band vs excitation power have been explored. It is found that the rise time of the upconversion fluorescence decay curve decreases gradually with the increase of the doped concentration of Sc3+, which confirms that the energy transfer rate (from Yb3+ to Er3+) obtains a significant increase by the introduction of Sc3+. It makes the population of 2H11/2/4S3/2 excited state easier than the 4F9/2 counterpart, then induces the considerable upconversion fluorescence regulation. As the emission color of the NaGdF4-based microcrystal is easy to adjust, it is excepted to show a great potential in the fields of fluorescence anti-counterfeiting, optical waveguide, and so on. The upconversion fluorescence regulation of single rare earth doped microcrystal induced by codoping with small radius ion can be applied to other luminous hosts.