For the typical process defects of semiconductor optical waveguide in the actual fabrication process, an effective analysis method is proposed based on the finite element method. For actual incident optical fields, the optical fields in waveguide are calculated for the first time when the defects exist. The effects of the defect position, size, type and wavelength of the incident light on the loss and mode coupling of semiconductor optical waveguide are analyzed. The results show that the waveguide transmission loss oscillates with defect size and light wavelength. The defect refractive index is larger, oscillation frequency is higher. When defects are moving from the core center to the edge, the oscillation of the transmission loss with waveguide structure size become monotone increasing. One part of the loss energy becomes the substrate radiation mode, and the other is coupled to high-order modes. The process defects make semiconductor optical waveguide loss increase greatly, the waveguide transmission mode is changed, and the integrated optical circuit performance is degraded significantly.