The data assimilation algorithm is a common algorithm in space weather research. In this paper, the time-frequency information in the dispersion spectrum of lightning whistlers received by the ZH-1 satellite is used as the observed value, and the international reference ionospheric model serves as the background model to construct the calculation model of the propagation time of lightning whistlers in the ionosphere. Kalman filtering is adopted to assimilate the electron density distribution along the propagation path of lightning whistlers. The results show that the situation where the electron density of the background model deviates greatly from the true value is significantly improved through data assimilation. The electron density after assimilation is in good agreement with the true value, which effectively helps realize the process of using observed values to correct the background value. On this basis, the influence of the frequency difference on the assimilation inversion effect is studied, and the results show that the assimilation effect is worse when the frequency difference between frequency points is less than 1 kHz.