The pore is the place where the seepage occurs in the porous medium, which is inevitably related to the permeability of the medium. Due to the special material source and formation process, coral sand has completely different pore characteristics compared with terrestrial sand. Through a series of microscopic studies, the reason for the special pore properties of coral sand in essence was revealed. It is found that it is reasonable to describe the properties of pores from the aspect of pore shape, pore throat size and global connectivity. Among them, pore shape is measured by the shape factor. Pore throat size includes pore radius and throat radius. Global connectivity in the porous media is described by coordination numbers. Particle shape and particle surface roughness are the main factors affecting pore shape, pore throat size and global connectivity. Particle shape mainly affects pore shape, throat size, pore throat size dispersion and the uniform distribution of connectivity in the medium. Particle surface roughness mainly affects pore shape, pore shape dispersion, pore size and global connectivity in the porous medium.