Upconversion nanoparticles (UCNPs) have attracted enormous interest over the past few years because of their unique optical properties and potential for use in various applications such as bioimaging probes, biosensors, and light-harvesting materials for photovoltaics. The improvement of imaging resolution is one of the most important goals for UCNPs used in biological applications. Super-resolution imaging techniques that overcome the fundamental diffraction limit of light rely on the photochemistry of organic dyes or fluorescent proteins. Here we report our progress toward super-resolution microscopy with UCNPs. We found that the red emission (655 nm) of core/shell UCNPs with the structure NaYF4:Yb3+,Er3+/NaYF4 could be modulated by emission depletion (ED) of the intermediate state that interacts resonantly with an infrared beam (1540 nm). In contrast, the green emission bands (525 and 545 nm) of the UCNPs were less affected by irradiation with the infrared beam. The origin of such distinct behaviors between the green and red emissions was attributed to their different photophysical pathways.