In the construction process of islands and reefs in the South China Sea, calcareous sand, as an important foundation and building material, has been widely used in engineering practice. It is crucial to explore the mechanical properties of calcareous sands to ensure the stability and maintenance of these islands and reefs. To study the effects of the bonding progressive failure on its macroscopic mechanical properties, a binary media bonding contact model is developed. This model can describe the gradual deterioration process of the intergranular cementation. Additionally, a discrete elemental contact subroutine (DLL) is created by C++ language program for the particle flow program (PFC2D) to utilize. The compression and direct shear testing of single contact was subjected. The computational accuracy of the proposed binary media contact model was confirmed by the comparison of the theoretical and numerical results. The biaxial shear discrete element simulations were conducted to study the behaviors of calcareous sand under different confining pressure conditions. The stress-strain curves obtained are in good agreement with the experimental results. The results show that the proposed binary media bonding contact model can accurately reflects the mechanical properties of calcareous sand. Based on calibrated discrete element contact mesoscopic parameters, the biaxial shear discrete element numerical simulations with different damage parameters were carried out. The effects of damage parameters on the stress-strain curves and shear strength are discussed. The evolution of effective coordination number, fabric anisotropy and force chain number are also analyzed. The research results can provide a basis for the study of macro-micromechanical properties of calcareous sand.