Lanthanide-doped upconversion nanoparticles have shown considerable promise in solid-state lasers, three-dimensional flat-panel displays, and solar cells and especially biological labeling and imaging. It has been demonstrated extensively that the epitaxial coating of upconversion (UC) core crystals with a lattice-matched shell can passivate the core and enhance the overall upconversion emission intensity of the materials. However, there are few papers that report a precise link between the shell thickness of core/shell nanoparticles and their optical properties. This is mainly because rare earth fluoride upconversion core/shell structures have only been inferred from indirect measurements to date. Herein, a reproducible method to grow a hexagonal NaGdF(4) shell on NaYF(4):Yb,Er nanocrystals with monolayer control thickness is demonstrated for the first time. On the basis of the cryo-transmission electron microscopy, rigorous electron energy loss spectroscopy, and high-angle annular dark-field investigations on the core/shell structure under a low operation temperature (96 K), direct imaging the NaYF(4):Yb,Er@NaGdF(4) nanocrystal core/shell structure at the subnanometer level was realized for the first time. Furthermore, a strong linear link between the NaGdF(4) shell thickness and the optical response of the hexagonal NaYF(4):Yb,Er@NaGdF(4) core/shell nanocrystals has been established. During the epitaxial growth of the NaGdF(4) shell layer by layer, surface defects of the nanocrystals can be gradually passivated by the homogeneous shell deposition process, which results in the obvious enhancement in overall UC emission intensity and lifetime and is more resistant to quenching by water molecules.