Phasor algorithm composed of two orthogonal filters is systematically expounded.Since the filtering characteristic of algorithm is connected with both frequency of the input signal and time parameter，the frequency characteristic of phasor algorithm is defined，which provides a method to estimate the filter capacity quantificationally.With the coefficient of window function as a parameter，the general discrete equation in time domain and maximum amplitude frequency characteristic of phasor algorithm based on sine and cosine filters are deduced.Taking interturn protection of generator as an example，a design method for seeking the optimum parameter of window function is proposed in allusion to the filtering requirement of some typical characteristic harmonic components in relay protection，which makes the algorithm efficiently filter the characteristic harmonic as well as suppress other non-characteristic harmonic components.