The phase-shift deformation patterns effectively demodulate from the deformed composite pattern when composite grating phase-measuring profilometry is used to perform a three-dimensional measurement; in this case, selection of the filtering window is considerably important. Further, a mixed window is proposed to improve the measurement accuracy by analyzing the characteristics of noise and their different effects on different orientations of the spectrum components and searching the best filtering window with respect to the spatial spectrum in two mutually orthogonal directions. The digital simulations show that the designed mixed window exhibits better noise suppression when compared with those exhibited by the rectangular, triangular, Blackman, and Hanning filtering windows. The measurement results obtained with respect to the known-height plane denote that the smallest reconstruction error can be obtained using the mixed window equalizing noise and spectral leakage. The root mean square error of the mixed window is reduced by 9.64% compared to that of the Hanning filtering window, and the measurement accuracy is effectively improved. Furthermore, the feasibility and effectiveness of the proposed method are verified via the physical measurement experiments.