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Photothermal therapy operated in the second near-infrared (NIR-II, 1000–1700 nm) window and fluorescence imaging in the NIR-IIb (1500–1700 nm) region have become the most promising techniques in phototheranostics. Their combination enables simultaneous high-resolution optical imaging and deep-penetrating phototherapy, which is essential for high-performance phototheranostics. Herein, carboxyl-functionalized small organic photothermal molecules (Se-TC) and multi-layered NIR-IIb emissive rare-earth-doped nanoparticles (NaYF₄:Yb,Er,Ce@NaYF₄:Yb,Nd@NaYF₄, RENP) were rationally designed and successfully synthesized. Then, high-performance hybrid phototheranostic nanoagents (Se-TC@RENP@F) were easily constructed through the coordination between Se-TC and RENP and followed by subsequent F127 encapsulation. The carboxyl groups of Se-TC can offer strong binding affinity towards rare-earth-doped nanoparticles, which help improving the stability of Se-TC@RENP@F. The multilayered structure of RENP largely enhance the NIR-IIb emission under 808 nm excitation. The obtained Se-TC@RENP@F exhibited high 1064 nm absorption (extinction coefficient: 24.7 L g⁻¹ cm⁻¹), large photothermal conversion efficiency (PCE, 36.9%), good NIR-IIb emission (peak: 1545 nm), as well as great photostability. Upon 1064 nm laser irradiation, high hyperthermia can be achieved to kill tumor cells efficiently. In addition, based on the excellent NIR-IIb emission of Se-TC@RENP@F, in vivo angiography and tumor detection can be realized. This work provides a distinguished paradigm for NIR-IIb-imaging-guided NIR-II photothermal therapy and establishes an artful strategy for high-performance phototheranostics. Full article