Fluorescence imaging technology has become a powerful tool for noninvasive in vivo detection due to its ability to offer immediate observations with high sensitivity and spatiotemporal resolution, In particular, fluorescence in the second near-infrared window (NIR-II, 1000−1700 nm) exhibits less interaction of scattering and absorption of photons in biological tissues than imaging in the visible range, resulting in deeper optical penetration depth and reduced autofluorescence interference, enabling higher imaging contrast. The long ends of the NIR-II (NIR-IIb, 1500−1700 nm) bands strike an optimal balance between photon scattering and water absorption effects, along with diminished autofluorescence. Rare earth-doped nanoparticles (RENPs) are ideal NIR-IIb imaging probes because of their NIR exaction bands, narrow emission bans, and excellent photostability. However, current NIR-IIb probes are mainly used for one-photon wide-field fluorescence imaging, complicated by intense out-of-focus background fluorescence, making three-dimensional (3D) imaging of living samples challenging. To overcome this, we propose a periodic line pattern to illuminate the sample and combine RENPs probes with emissions at NIR-IIb to realize 3D bioimaging in deep tissue using structured illumination microscopy (SIM). This approach can potentially enhance the penetration depth and spatial resolution in vivo 3D imaging by reducing photon scattering and autofluorescence in the NIR-IIb region and suppressing out-of-focus background signals in SIM.