Studies on Sc³⁺-based nanomaterials have been reported in recent years. However, most of the as-prepared nanomaterials are hydrophobic, thus complicated surface encapsulation renders them hydrophilic for biological applications. In our work, we used water soluble polyvinylpyrrolidone (PVP) as a chelating agent and a classic hydrothermal method to prepare water soluble cubic K₂NaScF₆ nanocrystals (NCs) for the first time. Different ratios of NH₄F/RE (3, 4, 5, 6) have been studied in the crystalline phase transformation from KSc₂F₇ to K₂NaScF₆ NCs. When the ratio is over 6, an unusual hexagonal NaYbF₄ phase separation phenomenon can be observed. In addition, Yb³⁺/Er³⁺ ion pairs have been doped into the K₂NaScF₆ NCs to verify that they are better up-conversion luminescence matrix materials than KSc₂F₇ NCs.