Abstract: Division-of-amplitude photopolarimeter(DOAP) was the key part of Stokes ellipsometer. To reach the complex and strict processing demands of beam splitter in DOAP, two waveplates are inserted respectively in the reflection light path and transmittion light path of classic DOAP to form an improved DOAP. The instrument matrix of new DOAP was derived and influence of waveplate parameters on the condition number of instrument matrix was also analyzed. From theoretical analysis and experimental verification, the optimal parameters and their relationships of waveplates were gotten. The results show that, measurement standard errors of film thickness and refractive index of the optimized Stokes ellipsometer are 0.1nm and 0.001 respectively. By choosing the optimal azimuthal angles or phase retardations of waveplates, the instrument matrix can be optimized to improve the accuracy and stability of measurement.