In this paper, we have studied the wavelength shift in a low-repetition-rate passively mode-locked fiber laser by nonlinear polarization rotation technique theoretically and experimentally. The central wavelength of the pulse can shift from 1563.0 nm to 1564.5 nm by adjusting the polarization controllers in the laser with a 1-km non-zero dispersion-shift fiber. Simulation results verify the experimental observations and the central wavelength shift is related to the cavity filter, which depends on the birefringence, nonlinearity and the length of fiber. The spectral filter effect is significant for the stability of the laser system besides excessive nonlinearity.