Abstract: In the short baseline multi-station joint positioning of skywave over-the-horizon-radar(OTHR) system, the ionospheric virtual height of different propagation links of radio waves is generally assumed to be equal. In order to search the effect of this assumption on the positioning results, we conduct observation experiments to study the influence of ionospheric virtual height on the accuracy of multi-station joint positioning. In the experiment, two receiver stations are set up to simulate the receiver station of the short baseline OTHR system, and then the target station is set up at a long distance. We simulate the reflected wave of the target by using the transmitted wave from the target station. This paper assumes that the ionospheric virtual height and the great circle distance of the link from the reference station to the target station are known. In this case, for the same operating frequency, the great circle distance between the positioning station and the target station is calculated by using the ionospheric reflected virtual height on the propagation link between the reference and target stations. The results show that when the distance between the reference station and the positioning station is about 90 km meanwhile the great circle distance between the target and the positioning station (Daofu-Wuhan) is about 1260 km, the root mean square error of the virtual height of the two links is about 5.82 km, the positioning root mean square error of the great circle distance is about 5.02 km, and the relative error is about 0.34%. When the great circle distance (Leshan-Wuhan) is about 1000 km, the errors are about 5.5 km, 5.69 km and 0.46%, respectively. The experimental results and theoretical analysis show that the accuracy of target positioning can be further improved by shortening the layout of receiving stations and reducing the ionospheric virtual height. The experimental results can provide some reference value for the construction of short baseline skywave OTHR.