Liquid crystal displays (LCDs) are used for projection in phase measuring deflection (PMD) surface shape detection. The multilayer transparent structure of the LCD refracts the light path, generating positional deviation errors. The error requires point-to-point correction to improve the final measurement accuracy. In this study, an equivalent transparent layer was modeled based on the LCD multilayer transparent structure, and a corresponding PMD model was established for analysis and compensation for the transparent layer. The standard spherical mirror and flat mirror were detected using a compensation algorithm to PMD. The root-mean-square (RMS) error of the surface shape decreases by 20%-40% compared with that before compensation. The error caused by the refraction effect of the LCD transparent layer in a single-screen PMD can be compensated using the proposed method. The RMS error is decreased, and the detection result is closer to the actual surface error after compensation than before compensation.