Calcareous sand is a special marine soil rich in calcium carbonate minerals, characterized by brittle particles. It is, therefore, widely used as a filling material in the construction of islands and reefs. In this study, a series of cyclic tri-axial tests were conducted on calcareous sand taken from a reef in the South China Sea under different confining pressures and cyclic stress ratio (CSR). Then, applying the shakedown theory, the cumulative deformation of calcareous sand under a long-term cyclic load of aircraft was evaluated. Results showed that with the increase in the effective confining pressure, the stress–strain curves of calcareous sand showed a change from the strain-softening to the strain-hardening state; the volumetric strain of calcareous sand showed a change from shear shrinkage and then shear expansion to continuous shear shrinkage. Calcareous sand showed three different response behaviors under cyclic load: plastic shakedown, plastic creep and incremental plastic failure. With the plastic strain rate as the defining index, this study determined the critical CSR of calcareous sand under different shakedown response statuses and found them to increase with the effective confining pressure. The empirical formula for critical stress was established based on the fitting analysis of critical CSR under different confining pressures, taking the confining pressure as the variable. At the early stage of the cyclic load, calcareous sand samples were under compression. When the resilient modulus grew rapidly and the number of loading cycles continued to increase, the particles of calcareous sand samples were crushed, causing the fine particles to fill the voids among coarse particles, further compacting the samples and increasing the resilient modulus of calcareous sand samples. Hardin’s breakage potential model was adopted to quantitatively describe the particle breakage of calcareous sand samples before and after tests. The results indicated that calcareous sand samples produced obvious particle breakage when the CSR was small. As the CSR increased, the extent of the breakage of the sample particles first increased and thereafter stabilized. This study provides a theoretical reference for the assessment of the dynamic stability of calcareous sand subgrade subjected to traffic loads.