The phase transition of upconversion nanocrystals (UNs) from cubic to hexagonal structure is of fundamental importance in improving the luminescence intensity by about one or two orders of magnitudes, but the mechanism is still not well understood and efforts to completely transfer the phase from cubic to hexagonal structure remains a difficult and challenging task. Here, we describe a hydrothermal system in which an anion induces the phase transition process to give simultaneous control over the size, morphology, phase and emission properties. We first confirm that the crystal cell oriented-rotation driven by an anion in a hydrothermal system promoted the phase transition, and the energy zones figure of the phase transition from cubic to hexagonal structure has been figured out. We have successfully applied the structural mechanics finite element calculations to validate the reaction process. We have also demonstrated that porous UNs can be rationally tuned in size (down to fifteen nanometers), phase (cubic or hexagonal) and emission properties at precisely defined conditions, and were effective for in vitro and in vivo CT imaging.