Lanthanide luminescence nanothermometers (LNTs) provide microscopic, highly sensitive, and visualizable optical signals for reporting temperature information, which is particularly useful in biomedicine to achieve precise diagnosis and therapy. However, LNTs with efficient emissions at the long-wavelength region of the second and the third near-infrared (NIR-II/III) biological window, which is more favourable for in vivo thermometry, are still limited. Herein, we present a lanthanide-doped nanocomposite with Tm3+ and Nd3+ ions as emitters working beyond 1200 nm to construct a dual ratiometric LNT. The cross-relaxation processes among lanthanide ions are employed to establish a strategy to enhance the NIR emissions of Tm3+ for bioimaging-based temperature detection in vivo. The dual ratiometric probes included in the nanocomposite have potential in monitoring the temperature difference and heat transfer at the nanoscale, which would be useful in modulating the heating operation more precisely during thermal therapy and other biomedical applications. This work not only provides a powerful tool for temperature sensing in vivo but also proposes a method to build high-efficiency NIR-II/III lanthanide luminescent nanomaterials for broader bio-applications.