Two-photon light sheet microscopy is widely used in biomedical related fields due to its advantages of high spatio-temporal resolution and low phototoxicity and photobleaching. However, due to the scattering and absorption of excitation light and fluorescence by biological samples, the quality of deep imaging of samples is poor, and it is difficult to realize large-sample, high-throughput imaging due to the narrow sample operating space of traditional light sheet microscopy. To address the above problems, we optimized the spatial layout of the light sheet microscopy system and combined it with a near-infrared II excitation light source, and at the same time, we used an axicon to modulate the ordinary Gaussian illumination beam into a Bessel beam, which achieved a wide range of thin-sheet illumination by virtue of its non-diffractive properties, and finally constructed an open-top two-photon light sheet imaging system based on non-diffractive Bessel beam. The lateral and axial resolutions of the system are (1.85 ± 0.09) μm and (3.23 ± 0.32) μm, respectively, and the field of view is greater than 600 μm, achieving three-dimensional high-resolution imaging. The experiment completed deep tissue imaging of acute kidney injury mice, obtained a large amount of vascular structural information, which facilitates the revelation of pathological changes in acute kidney injury tissues. The experimental results not only contribute to a better understanding of the pathogenesis of acute kidney injury, but also provide a reference basis for future clinical diagnosis and treatment, validating the potential of open-top near-infrared II Bessel two-photon light-sheet microscopy for three-dimensional pathological evaluation.