A novel OA/ionic liquid two-phase system combining the merits of thermal decomposition method, the IL-based strategy, and the two-phase approach is introduced to synthesize high-quality lanthanide-doped NaGdF4 upconversion nanocrystals with different crystal-phases in OA-phase and IL-phase through a one-step controllable reaction. Oil-dispersible cubic-phase NaGdF(4):Yb, Er (Ho, Tm) nanocrystals with ultra-small size (similar to 5 nm) and monodispersity are obtained in the OA phase of the two-phase system via an IL-based reaction. More importantly, water-soluble hexagonal-phase NaGdF4:Yb, Er nanocrystals are obtained in the same system simply by adopting an extremely facile method to complete the dual phase-transition (crystal-phase transition and OA-phase to IL-phase transition) simultaneously. The synthesized lanthanide-doped NaGdF(4) upconversion nanocrystals are effective for dual-mode UCL imaging and CT imaging in vivo.