Phase-shifting interferometry is widely used in the surface measurement of optical elements as its high precision. The phases obtained from phase-shifting algorithms are wrapped between -π and π. The algorithm based on the region growing theory (seed point algorithm) can realize phase unwrapping of connected regions with high precision. The algorithm based on discrete cosine transform (DCT) algorithm can realize phase unwrapping of rectangular region. In practical measurements, the valid region of test flat is often non-rectangular and separated. On the basis of analyzing the advantages and disadvantages of the above algorithms, the seed point unwrapping algorithm based on DCT algorithm is presented. Firstly, the wrapped phases are unwrapped totally with DCT algorithm. Secondly, the wrapped phases of separated regions are unwrapped with the seed point algorithm respectively. Then they are unified with the interference orders obtained from DCT algorithm. The experimental results show that the algorithm overcomes the disadvantages of the seed point algorithm and DCT algorithm. It can unwrap the wrapped phases obtained from separated interferograms correctly and quickly, and it is more stable and more precise than the two algorithms above.