A phase unwrapping method used in the spectral domain phase microscopy (SDPM) is proposed. A wrapped phase with a small noise and an unwrapped phase with a big noise are obtained by using respectively the Fourier transform (FT) method and the synthetic-wavelength phase calculation method. The wrapped number of the wrapped phase is calculated from the difference between the unwrapped and wrapped phases, and thus the unwrapping of the wrapped phase with a small noise is conducted. The presented method eliminates the boundary segmentation error introduced in the existing phase unwrapping methods. An SDPM system based on synthetic-wavelength is established. A piezoelectric translation stage is used to quantitatively verify that this system is capable of accurately unwrapping the phase with a large gradient boundary. The phase imaging of red blood cells and tilted mirror surfaces is also performed. The displacement sensitivity of this system in air is 0.043 nm.