Upconversion phosphors composed of both gray-white and gray-black microcrystals were synthesized using a facile hydrothermal route. The microcrystals with different contrast in the SEM images were confirmed to be Y-based and Sc-based microcrystals by SEM, XRD, EDX and elemental mapping. The morphology evolution of Y-based microcrystal induced by Sc 3+ co-doping can be ascribed to the variation of anisotropic growth for different crystal planes. We studied the dependence of fluorescence intensity on pump power and investigated the variation of fluorescence decay dynamics for the different compositions. It was found that an increase of the energy transfer rate from Yb 3+ to Er 3+ , Ho 3+ , Eu 3+ and Tm 3+ , and a decrease of the phonon energy by Sc 3+ co-doping were responsible for the observed fluorescence tuning. Such a simultaneous morphology evolution and upconversion fluorescence tuning of single Y-based fluoride microcrystal with low phonon energy will show a great potential in microlaser, photovoltaics, and photo-communication.