In the present paper, the four-wave mixing principle of fiber was analyzed, and the high-gain phase-matching conditions were shown. The nonlinear coefficient and dispersion characteristics of photonic crystal fibers were calculated by multipole method. The phase mismatch characteristics of fibers with multiple zero-dispersion wavelengths were analyzed for the first time. The changing rules of phase matching wavelength with the pump wavelength and the pump power were obtained, and the phase matching curves were shown. The characteristics of phase matching wavelengths for different dispersion curves were analyzed. There are four new excitation wavelengths of four-wave mixing spectrum in two zero-dispersion wavelength photonic crystal fibers. Four-wave mixing spectroscopy of photonic crystal fibers with two zero-dispersion wavelengths was obtained in the experiment, which is consistent with the theoretical analysis, and verified the reliability of the phase matching theory. The fiber with multiple zero-dispersion wavelengths can create a rich phase-matching topology, excite more four-wave mixing wavelengths, enabling enhanced control over the spectral locations of the four-wave mixing and resonant-radiation bands emitted by solitons and short pulses. These provide theoretical guidance for photonic crystal fiber wavelength conversion and supercontinuum generation based on four-wave mixing.