Upconversion nanoparticles (UCNPs) have shown considerable promises in many fields; however, their low upconversion efficiency is still the most serious limitation of their applications. Herein, we report for first time that the homogeneous doping approach based on the successive layer-by-layer method can greatly improve the efficiency of the UCNPs. The quantum yield as high as 0.89 ± 0.05% is realized for the homogeneous doping NaGdF4:Yb,Er/NaYF4 UCNPs, which is nearly 2 times higher than that of the heterogeneous doping NaGdF4:Yb,Er/NaYF4 UCNPs (0.47 ± 0.05%). The influences of spatial distributions and local relative concentrations of the dopants on the optical properties of UCNPs were investigated in the single particle level. It was found that heterogeneous doping indeed existed during the spontaneous growth process of the nanoparticles. The heterogeneous doping property can further induce many negative effects on the optical properties of UCNPs, especially the luminescent efficiency. The spatial distributions and local relative concentrations of the dopants can be well controlled by the successive layer-by-layer homogeneous doping method on the monolayer level and homogeneously distributed in the single particle level. Furthermore, by using homogeneous doping NaGdF4:Yb,Tm as initial core, the multicolor emission intensity of NaGdF4:Yb,Tm/NaGdF4:A (A = Tb3+, Eu3+) core/shell nanoparticles can also exhibit 20%–30% improvement. We believe that such a homogeneous doping model can open the door to improve the upconversion optical properties by engineering the local distribution of the sensitizer, activator, host, etc., in a microcosmic and provide a track for engineering the high quality UCNPs with advanced nanostructure and optical properties.