Red-emitting phosphors play a vital role in reinforcing the quality of phosphor-converted white light-emitting diodes. Unfortunately, concentration quenching and unsatisfied thermal stability are still the inevitable shortcomings of the red-emitting phosphors. Herein, we utilized phase transition to simultaneously tailor the concentration quenching and thermal stability of Eu3+-activated NaYbF4 (NaYbF4:xEu3+) nanoparticles, in order to overcome these limitations. With the increasing doping level, the resultant samples undergo a phase transition from cubic to hexagonal phase. Notably, the optimal doping content for Eu3+ in the NaYbF4 nanoparticles with cubic phase is 30 mol%. However, when the phase transition occurs, the concentration quenching takes place at a much higher doping concentration, i.e. the optimum content of Eu3+ in the structure is increased to about 80 mol%. Moreover, with elevating the Eu3+ content, the local coordination environment of Eu3+ in the NaYbF4 host lattice is changed from inversion (centrosymmetric) to non-inversion symmetry (non-centrosymmetric), which is further confirmed by the theoretical calculation results via Judd-Oflet theory. Furthermore, compared with cubic samples, the hexagonal NaYbF4:0.8Eu3+ nanoparticles show improved thermal stability. Importantly, utilizing hexagonal NaYbF4:0.8Eu3+ nanoparticles, a designed white light-emitting diode emits warm white light, with desired color coordinates (0.398,0.374), high color rendering index (86.3), and low correlated color temperature (3537 K). Besides, NaYbF4:xEu3+ nanoparticles and their flexible polydimethylsiloxane films exhibit potential applications in high-temperature optical anti-counterfeiting. This work may support a new perspective for tailoring the concentration quenching and thermal stability of various phosphors.