In this paper, we propose a new method for three-dimensional (3D) visualization that proportionally estimates the number of photons in the background and the object under photon-starved conditions. Photon-counting integral imaging is one of the techniques for 3D image visualization under photon-starved conditions. However, conventional photon-counting integral imaging has the problem that a random noise is generated in the background of the image by estimating the same number of photons in entire areas of images. On the other hand, our proposed method reduces the random noise by estimating the proportional number of photons in the background and the object. In addition, the spatial overlaps have been applied to the space where photons overlap to obtain the enhanced 3D images. To demonstrate the feasibility of our proposed method, we conducted optical experiments and calculated the performance metrics such as normalized cross-correlation, peak signal-to-noise ratio (PSNR), and structural similarity index measure (SSIM). For SSIM of 3D visualization results by our proposed method and conventional method, our proposed method achieves about 3.42 times higher SSIM than conventional method. Therefore, our proposed method can obtain better 3D visualization of objects than conventional photon-counting integral imaging methods under photon-starved conditions.