Yb3+/Er3+-co-doped cubic NaYF4 and Yb3+/Er3+/Gd3+-tri-doped hexagonal NaYF4 nanocrystals were synthesized by a modified coprecipitation method with ethylenediamine tetraacetic acid (EDTA) as chelating agent. The samples’ morphology, crystal phase and upconversion emission were measured with transmission electron microscope (TEM), X-ray diffraction patterns (XRD) and upconversion luminescence spectrum. TEM and XRD results showed that the phase transition from cubic to hexagonal was promoted through Gd3+ doping. It has been reported that the upconversion efficiency of hexagonal NaYF4 is higher than that of cubic NaYF4, however, the effect of crystal phase on upconversion luminescence has not been well understood. This work focuses analysis of measurement results to compare the effect of crystal phase on the crystal field energy splitting and upconversion emission intensity as well as emission color, and a mechanism of luminescence enhancement and color tunability are revealed. Strong visible upconversion luminescence can be seen clearly by the naked eyes in both cubic phase and hexagonal phase samples upon excitation by a 980 nm laser diode with power of 10 mW, consisting of green emissions centered at around 525/550 nm originating from the transitions of 2H11/2/4S3/2→4I15/2 and red emission at about 657 nm from 4F9/2 to 4I15/2 of Er3+ ions respectively. In comparison to cubic sample, the hexagonal phase sample presented much stronger and sharper upconversion luminescence, whose emission efficiency was enhanced 10 times with an additional transition of 2H9/2→4I13/2 at 557 nm, furthermore, the intensity ratio of red to green emission increased from 2∶1 to 3∶1. Doping NaYF4 nanocrystals with Gd3+ ions induced the hexagonal-to-cubic phase transition and thus decreased the crystal symmetry, consequently increased absorption cross-section and 4f—4f transition probabilities by relaxing forbidden selection rules, resulting in stronger emission. In the mean time, the decreasing unit-cell volume of the hexagonal phase increased the crystal field strength around the dopant ions and consequently led to that hexagonal phase samples present much sharper emission compared to cubic counterparts. It demonstrates that phase transition can tune crystal field energy splitting, luminescence intensity and emission color.