The phase unwrapping method based on the polar coordinate to get the alignment offset was proposed for the wrapped phase generated after the single closed interference fringe phase extraction in alignment of nanolithography. The phase distribution of the fringe pattern occurs in the relative movement between two circular gratings was transformed from rectangular coordinates system to polar coordinates system firstly; then the relationship between the alignment offset and the phase parameter was analysis in polar coordinates system; the initial phase amplitude and phase delay in different radial radius were got to acquire the alignment offset finally. The feasibility of the method was verified by numerical simulation and experiment and the comparisons of the tradition least squares method and path tracking method are given. The results show that the wrapped phase can be unwrapped for the alignment with high precision in tens of nanometers through the method with good adaptability.