The phase characteristic of two dimensional hexagonal photonic crystal with near-zero refractive index is investigated by finite-difference time-domain (FDTD) method. A new method to calculate the equivalent refractive index is proposed by using the spatial spectrum of electric field phase. The proposed method can directly reflect the change of the electric field phase, which clarifies the transmission mechanism of the negative refraction. By this method, the influences of the wavelength of transverse magnetic (TM) mode and temperature on equivalent refractive index are studied.