Modern nanotechnology increasingly demands multifunctional nanomaterials, motivating rational core-shell designs to integrate diverse capabilities within a single nanostructure. Herein, core-shell-shell structured NaYF4:20%Yb3+@NaErF4:0.5%Tm3+@NaGdF4:20%Yb3+ nanoparticles are developed through a layer-by-layer epitaxial growth strategy. The key novelty of this synthesis lies in the precise spatial organization of functional ions: an inner core and an outer shell rich in Yb3+ sensitizers collaboratively pump a central energymigrating erbium sublattice. This unique architecture exhibits intense red upconversion luminescence under 980 nm excitation while enabling multimodal nanothermometry and dual-modal bioimaging (optical imaging and T1-weighted magnetic resonance imaging). Aberration-corrected transmission electron microscopy (ACTEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) analyses confirm the precise layered architecture and high crystallinity. Significantly, the outer thin shell induces anomalous thermal enhancement at 544 nm. This phenomenon is governed by a shell-thickness-mediated energy migration process, which modulates the interaction between the erbium sublattice and surface ligands, thereby facilitating enhanced performance in multimodal nanothermometry. HAADF-STEM provides direct visualization of shell thickness variations, offering mechanistic evidence for this phenomenon. Crucially, dual-modal bioimaging capability is validated in vivo. This core-shell design strategy advances the development of multifunctional nanoparticles for nanothermometry and bioimaging applications.