Ionosperic sporadic-E layer (Es layer) is the irregular structure in ionosphere which often occurs in summer of China, but the current model of height estimation with high frequency rays does not consider the Es layer, which often makes a large error in the estimation of the target height. In this paper, the parameters of the actual ionosphere are analyzed by using the measured data of the ionospheric vertical measurement station and the information about the variation of the ionosphere in southeastern China which was obtained in recent years. The measured data indicate that the probability of occurrence of Es in China is relatively high, especially in summer. When Es appears in summer, the probability of its cut-off frequency greater than 4.5 MHz reaches up to 83.6%, therefore, it is necessary to study the target height measurement model and algorithm when the ionosphere contains Es. Firstly, on the basis of the quasi-parabolic segments ionosphere model and real ionosphere parameters, the ionosphere model containing the Es layer is established. In this model, Es layer and its connection layer with the E layer are represented by parabola and reverse parabola respectively. Then, the high frequency transmission characteristics of the target micro multipath are analyzed based on Es model. The simulation shows that 4 multipath echoes can be simulated by the characteristics of different slant ranges and Doppler frequencies in the multiple echoes of the target. By matching the simulated 4 multipath echoes with the actual high frequency echo of the target, when the matching degree reaches a maximum value, the estimated height value can be obtained. Finally, based on the micro multipath difference between high frequency rays and the ionospheric model with Es layer, a height estimation method using matched-field processing and hill climbing search algorithm is proposed. This method can greatly reduce the search time for obtaining the real height value. Through theoretical analysis and experimental verification, the relationships between the ionospheric plasma frequency and height, between the transmission path of high frequency rays and the elevation angle/transmitting frequency, and between the micro path characteristics of high frequency rays and the height of target are obtained. Ionospheric model with the Es layer and the new target height measurement method based on the matched-field processing can accurately estimate the height of the target and have a faster calculation speed.