The invention discloses a method for determining a Kalman filtering state error covariance matrix in ionospheric modeling. The method comprises the following steps: performing epoch difference on eachionospheric spherical harmonic coefficient Ci; calculating the change rate of the spherical harmonic coefficient of the ionized layer in the Kalman filtering epoch interval; calculating the standarddeviation of the ionized layer spherical harmonic coefficient change rate vCi (k) sequence; and obtaining a Kalman filtering state error covariance matrix Q in ionospheric modeling, wherein Q is a diagonal matrix, and diagonal elements are squares of three times of the standard deviation of the spherical harmonic coefficient change rate vCi (k) of each ionospheric modeling. The method provided bythe invention is different from an existing pure experience determination method, calculates Q according to the spherical harmonic coefficient of the ionized layer, and can accurately give the variance of each element in the spherical harmonic coefficient of the ionized layer.