In the target localization of skywave over-the-horizon radar (OTHR), the error of the ionospheric parameters is one main error source. To reduce the error of ionospheric parameters, a method using both the information of reference sources (e.g., terrain features, ADS-B) in ground coordinates and the corresponding OTHR measurements is proposed to estimate the ionospheric parameters. Describing the ionospheric electron density profile by the quasi-parabolic model, the estimation of the ionospheric parameters is formulated as an inverse problem, and is solved by a Markov chain Monte Carlo method due to the complicated ray path equations. Simulation results show that, comparing with using the a prior value of the ionospheric parameters, using the estimated ionospheric parameters based on four airliners in OTHR coordinate registration process, the ground range RMSE of interested targets is reduced from 2.86 to 1.13 km and the corresponding improvement ratio is up to 60.39%. This illustrates that the proposed method using reference sources is able to significantly improve the accuracy of target localization.