Luminescence quench is common in overdoped upconversion nanoparticles. Various methods have been proposed to counteract the adverse effects of concentration quenching on luminescence, but in upconversion nanoparticles that are highly doped with both sensitizers and activators, the factors that contribute to the diminishing of the emission cannot be summarized by a single cause. Herein, a core–shell design is used to spatially separate the sensitizer (Yb³⁺) and activator (Er³⁺) and to modulate the emission by changes in the distribution position as well as the concentration of the dopant ions in order to probe the factors affecting the luminescence. When the sensitizer ions are located in the core, the luminescence intensity of the nanoparticles is significantly weaker than that of the other distribution, which implies that the effect of sensitizer and activator on luminescence in the highly doped state has a different and more complex mechanism. The intensity of the emission is more affected by Yb³⁺ than Er³⁺, which includes not only the self-quenching of Yb³⁺, but also the dominance in the Yb³⁺–Er³⁺ cross-relaxation. In this finding may provide new ideas for revealing the reasons for the diminished luminescence of highly doped upconversion nanoparticles and thus for enhancing luminescence.