In this paper, we propose three-dimensional (3D) photon counting integral imaging by using multi-level decomposition such as discrete wavelet transform to improve the visual quality and measurement accuracy under photon-starved conditions. Conventional 3D integral imaging can visualize 3D objects and acquire their depth information. However, the amount of irradiated light on the object causes the degradation of visual quality for 3D images under photon-starved conditions. To visualize 3D objects, photon counting integral imaging has been utilized. It can detect photons from 3D scenes by using a computational photon counting model, which is modelled by the Poisson random process. However, photons occur not only from objects but also in areas where objects do not exist. Moreover, photon fluctuation may occur in the scene through shot noise. Since these noise photons are measurement errors, it may decrease the image quality and accuracy. In contrast, our proposed method uses 2D discrete wavelet transform, which can emphasize the object photons effectively. Finally, our proposed method can enhance the visual quality of 3D images and provide more accurate depth information under photon-starved conditions. To prove the feasibility of our proposed method, we implement the optical experiment and calculate various image quality metrics.