The invention relates to a water soluble NaYF4@NaGdF4 nanocrystalline with an upconversion core-shell structure and a preparation method thereof, and belongs to the technical field of microwave polyhydric alcohol chemical method synthesis. The nanocrystalline with the upconversion core-shell structure provided by the invention, is regulatable balls with different sizes in addition amount of an outer polytetrafluorogadolinium sodium shell, and the average diameter is 14-38 nanometers. The physical phase is converted from square phase to hexagonal phase. According to the nanocrystalline with the core-shell structure provided by the invention, polyethyleneimine covers the surface of the polytetrafluorogadolinium sodium nanocrystalline, so that the particles have good water solubility, and the shape of products can be controlled, and the nanocrystalline has good biological compatibility. Along with increase of the shell layer, upconversion luminescence is increased, and the fluorescent lifetime cancellation time is prolonged. The nanocrystalline can be used as an effective CT (Computed Tomography) responder and has potential application value in the fields such as biological imaging. The nanocrystalline with the core-shell structure has higher fluorescence efficiency and better water solubility and biological application value.