The invention relates to a pilot frequency design method which is based on the assistance of pilot signal. The method comprises the following steps: pilot main sequence of a district and a pilot auxiliary sequence meet a certain of phase-shift relationship, pilot matrixes of an object district and an adjacent district are designed, and the adjacent district is led to have the same pilot structure with the object district, and the matrix of the adjacent district and the matrix of the object district meet the relationship that mean square error of least square estimation value which is responded by a channel of the object district is led to be minimum, and channel response of the object district is obtained through calculating. When the invention designs the pilot matrix of the adjacent district and the pilot matrix of the object district, the pilot matrixes are requested to meet the relationship that mean square error of least square estimation value which is responded by a channel of the object district is led to be minimum, and the error of a disturbance area to the object area is led to be the minimum, and the channel model which is established inhibits the disturbance between adjacent districts in maximum.