For precise optical elements, the size of in-surface defects is at the nanometer scale. When incident light illuminates in-surface defects on optical elements, strong diffraction and scattering effects are produced, and this greatly reduces the beam quality in optical systems. In this study, a three-dimensional model of the in-surface defects of K9 optical components was established. On this basis, a theoretical model of electromagnetic scattering between the defect and the incident and scattering fields was constructed. The 4 × 4-order scattering Mueller matrix light field distributions of incident light modulated by different-sized defects were obtained by numerical simulations, and the influencing factors were analyzed. These simulations provide a theoretical basis and a reference for the manufacture of precision optical elements and a scale calibration for surface quality detection methods.