The invention relates to a full phase difference detection method and system of electric power signals. The method comprises the steps that direction outputting is carried out on a forward signal sequence obtained by sampling to generate an inverse sequence; the forward signal sequence and the inverse sequence are respectively truncated to generate two groups of truncated signal sequences; a cosine function and a sine function of a tested reference frequency are respectively multiplied by the forward signal sequence, the inverse sequence and the two groups of truncated signal sequences to generate four groups of real frequency vector sequences and imaginary frequency vector sequences; digital filtering is carried out on the four groups of real frequency vector sequences and imaginary frequency vector sequences to generate four groups of imaginary number vector filtering sequences and real number vector filtering sequences, and four groups of imaginary number vector integral values and real number vector integral values are further generated by integration; and the four groups of imaginary number vector integral values and real number vector integral values are converted into four phases, the four phases are converted into an initial phase and a cut-off phase, and the difference of the cut-off phase and the initial phase is converted into a full phase difference. According to the invention, the full phase difference relatively high in accuracy can be obtained.