This paper proposes a new virtual ionospheric height model for over-the-horizon radar (OTHR) target tracking. Considering the spatial correlation of different ionosphere site, the virtual ionospheric heights are modeled by a Gaussian Markov random field (GMRF). The priors of the GMRF model can be learned from the historical measurements from ionosondes. Given the acquired measurements of the ionosphere subregions, the virtual ionospheric heights of the unmeasured subregions are inferred based on the GMRF model. Then we present the multipath probabilistic data association for uncertain coordinate registration (MPCR) with the new virtual ionospheric height model. Numerical simulation shows that the accuracy of OTHR target tracking is improved.