The construction of core-shell structures with multiple heterojunctions facilitates ion energy transfer and minimizes surface quenching effects, which are essential for enhancing and regulating the upconversion emission of materials. In this study, we effectively regulated the spatial distribution of Yb3+ and Er3+ ions in multilayered heterogeneous core-shell structures to significantly enhance the red upconversion emission of Er3+ ions. Specifically, the red emission intensity of the NaErF4@NaYbF4: 2 %Er3+@NaYF4 core-shell nanoparticles was enhanced nearly 24.4-fold compared to that of NaErF4 nanoparticles. This enhancement results from a bidirectional energy transfer process. Moreover, when we swapped the positions of the NaErF4 core and the NaYbF4: 2 %Er3+ shell and introduced NaYF4 inert isolation layer and Yb3+ ions, the red emission intensity of the NaYbF4:2 %Er3+@NaYF4:20 %Yb3+@NaErF4@ NaYF4 multilayer core-shell structure increased significantly by nearly 254.3-fold compared to NaErF4 nanoparticles. The remarkable enhancement of the red emission of Er3+ ions is primarily attributed to a well-organized bidirectional energy transfer process between the heavily doped core and shell Er3+-Yb3+ ion pairs. The energy transfer behavior of these multi-heterojunction core-shell nanoparticles was studied based on their spectral characteristics. The multilayer heterogeneous core-shell nanoparticles exhibited colorful emissions under different excitation conditions, highlighting their potential for biomedical applications and colorful anti-counterfeiting.