Neutron irradiation induced degradation of porous silica film is studied by Molecular Dynamics and Density-Functional theory-based methods. The degradation of microscopic structure, thermal property, and optical property of porous silica film are systematically investigated. Low-energy recoil is used to simulate the neutron irradiation effect. The pair and bond angle distributions, and coordination number distributions reveal that, under neutron irradiation, the microscopic structure of porous silica film is obviously modified, and the coordination defects are induced. We find that the higher recoil energy, the more coordination defects are formed in the film. The increased defects lead to a decrease in thermal conductivity. In addition, neutron irradiation induces additional optical absorption peaks in UV region and increasement in refractive index, resulting in a noticeable reduction in light transmittance. The detailed calculation of density of states reveals that these optical absorption peaks originate from the irradiation induced defect states in band gap. Our work shows that low-energy neutron irradiation can induce obvious defect density and degrade thermal and optical properties of porous silica film, which are responsible for subsequent laser-induced damage.