Based on the theoretical analysis of phase-shifted long-period grating, the transmission spectrum of phase-shifted long-period grating is studied by transfer matrix method. The impacts of magnitude of phase shift, change of average refractive index and length of grating on transmission spectrum of phase-shifted long-period grating are discussed. According to the rules, the structure parameters of phase-shifted long-period grating are properly adjusted to make its transmission spectrum correspond with the target spectrum for flattening EDFA to some extent. Maximum fluctuation of flattened gain spectrum of EDFA does not exceed ±0.7 dB in the range of 34 nm. The gain flattening filter designed by this method only contains one device, and it has favorable market prospects due to small size and ease of manufacturing and packaging.