To investigate the effect of crystal defects on properties of HMX-based polymer bonded explosive (PBX), two defect-free models and four defective models were established. Using molecular dynamics (MD) method, different models were simulated and the sensitivity, binding energy, detonation performance and mechanical properties of different models were calculated and compared. Results show that the crystal defects cause the interaction energy of trigger bond and cohesive energy density to decrease by 2.46-5.72 kJ·mol^-1 and 0.0251-0.0544 kJ·cm^-3, respectively, indicating that the sensitivity of defective models is increased and safety is decreased. The binding energy of defective models is decreased by 106.89-231.65 kJ·mol^-1, meaning that their stability is deteriorated. The density, detonation velocity and detonation pressure of defective models are decreased by 0.01-0.05 g·cm^-3, 36.35-185.69 m·s^-1 and 0.36-1.79 GPa, respectively. However, the variation of oxygen balance and detonation heat can be negligible. The variation of detonation parameter indicates that the damage power of defective models is weakened. Tensile modulus, bulk modulus, shear modulus of defective models are decreased by 0.062-1.772, 0.261-1.188 GPa and 0.012-0.685 GPa, respectively. The ratio of bulk modulus to shear modulus is increased by 0.002-0.366. The Cauchy pressure of dislocation and vacancy defective models is decreased by 0.822 GPa and 0.479 GPa, while it is increased by 0.114 GPa and 0.491 GPa in doping and twin defective models respectively, indicating that the deformation resistance of the defective models is decreased and the flexibility is enhanced.