In this manuscript, Ni2+ ions-doped NaYF4:Yb3+/Er3+ nanoparticles have been synthesized via a modified hydrothermal method. The upconversion luminescence intensities of the green (G) and red (R) emission of NaYF4:Yb3+/Er3+ co-doped with 20 mol% Ni2+ ions are the strongest which increase 32.84 and 20.99 times than that without doping Ni2+, respectively. In addition, the R/G ratio decreases with the concentration of Ni2+ increasing from 0 to 40 mol%. The underlying reason for luminescence enhanced and the R/G ratio decreased by Ni2+ doping is explored by a series of controlled experiments, and the mechanism based on the crystal field asymmetry, different substitution by Ni2+, the energy transition of Er3+ is studied in detail. The study indicates that the misshapen crystal field plays an important role in enhancement fluorescence emission, and several factors affect the R/G ratio including the crystal field, the substitution site and the energy transition. Our result may play a certain function for study and design of high-performance upconversion materials.