To realize long-distance, highly sensitivity three-dimensional imaging, photon counting computational ghost imaging has been researched in experiments. Structured light illumination is realized using an amplitude-type spatial light modulator based on a discrete cosine transform matrix or Walsh transform matrix as the measurement basis, and single-photon detection technology is used to achieve a 700 m distance, highly sensitivity three-dimensional imaging. Two algorithms, fast Fourier transform and iterative optimization, are researched and compared. The error in images reconstructed by the discrete cosine measurement basis is smaller than that in images reconstructed by the Walsh observation matrix under the same sampling rate, while the resolution of images reconstructed by the Walsh observation matrix is higher. Theoretically, the resolution of the computational ghost imaging system is not restricted by the diffraction limit of the receiving lens; however, resolution is still affected by the collection efficiency of the receiving lens, the counting rate of the single-photon detector, and exposure time, among others. We demonstrated that the imaging resolution of our experimental system improved on the Rayleigh diffraction limit resolution of the receiving lens by a factor of two. The photon counting computational ghost imaging scheme has the potential to visualize the imaging target in three dimensions under weak illumination, without the need of a rotating platform and scanning mirror. Our research method has reference value for research on single-pixel imaging technology based on photon counting and computational ghost imaging technology.