Defects produced by ion irradiation are effective to modulate many physical properties of phosphorene. In this paper, the molecular dynamics method is used to simulate the ion irradiation process of phosphorene. The relationships between the formation probability of defects and the energy of incident ions, ion species and incident angle of ions are revealed. The non-equilibrium molecular dynamics simulation is applied to calculate the thermal conductivity of irradiated phosphorene. The effects of the energy of ions, the irradiation dose, the type of ions and the incident angle of ions on the thermal conductivity of phosphorene are systematically investigated. The influence of the vacancies on the phonon participation rate of phosphorene is studied by lattice dynamics method, and the spatial distribution of localized modes is demonstrated. Based on the quantum-mechanical perturbation theory and bond relaxation theory, we point out that the dominant physical mechanism of vacancy defects which significantly reduce the thermal conductivity of phosphorene is the strong scattering of phonons by the low-coordinated atoms near the vacancies. This study provides a theoretical basis to tune the heat transport properties of phosphorene by defect engineering.