The surface shape and optical thickness variation of a lithium niobate (LNB) wafer were measured simultaneously using a wavelength-tuning interferometer with a new phase-shifting algorithm. It is necessary to suppress the harmonic signals for testing a highly reflective sample such as a crystal wafer. The LNB wafer subjected to polishing, which is in optical contact with a fused-silica (FS) supporting plate, generates six different overlapping interference fringes. The reflectivity of the wafer is typically 15%, yielding significant harmonic signals. The new algorithm can flexibly select the phase-shift interval and effectively suppress the harmonic signals and crosstalk. Experimental results indicated that the optical thickness variation of the LNB wafer was measured with an accuracy of 2 nm.