Near-infrared II (1000–1700 nm) three-dimensional (3D) microscopy addresses a significant improvement on the penetration depth for bioimaging, but is challenging in high z-direction spatial resolution, leading to imaging distortion in deep tissue bioimaging. Here, we developed Airy beam-assisted NIR-II light-sheet Microscope (NIR-II Airy LSM) to improve z-direction spatial resolution with large field of view (FOV) on thick biological specimens via self-healing properties of the propagation-invariant field. The axial resolution was measured to be consistently 3.5 µm across the whole FOV (∼ 600 µm), about 4 times higher than traditional Gaussian-beam based microscopy (∼ 15 µm). Besides, the NIR-II Airy LSM demonstrates 2–3 times higher signal background ratio (SBR) than NIR-I imaging, at the penetration depth of approximately 2.5 mm. The increased spatial resolution and SBR allows us to observe pathological conditions and progression of glomeruli and tubules of radiation induced kidney injury and discriminated integral damage degree of intestinal mucosal cells from intestinal tissue accurately via 3D volumetric multiplexed imaging. The improved NIR-II light-sheet microscopy exhibit complete 3D imaging capabilities of whole bio tissues without sacrificing axial resolution and avoid imaging distortion under deep tissue.