In order to investigate the physical and mechanical characteristics of coral reefs with different depth in the South China Sea, scanning electron microscopy (SEM) and X-ray tomography (CT) technology are used to characterize the micro morphology and internal pore structure characteristics of shallow and deep reef limestone. Quantitative relationships between P-wave velocity and porosity as well as density were established. Uniaxial compression tests on dry and saturated reef limestone were also carried out. Results show that shallow reef limestone is porous with excellent pore connectivity, and the main mineral composition is aragonite, which belongs to the biological sedimentary rock. While deep reef limestone is dense with poor pore connectivity, and the main mineral composition is calcite, belonging to the metamorphic rock. The porosity of deep reef limestone is about 1/10, with an average peak compressive strength of about 4.8 times and an average elastic modulus of about 4.5 times that of shallow reef limestone. Reef limestone belongs to soft or extremely soft rock, characterized by brittle destruction property. The typical damage pattern is multiple rupture surface destruction along the primary pore, growing line of corals and weak bond surface, with high residual strength. The hydrogenic effect of reef limestone is significant, and the water rationality of deep reef limestone is stronger than shallow reef limestone. The significant difference of physical and mechanical performances in shallow and deep reef limestone are mainly due to the variety in mineral components, pore structure and lithology caused by the varying degree of rock cementation with different depths.