Estimation of genomic breeding values is the key step in genomic selection. Many methods have been proposed for continuous traits, but methods for threshold traits are still scarce. Here we introduced threshold model to the framework of genomic selection, and specifically we extended the three Bayesian methods BayesA, BayesB and BayesCπ based on threshold model for estimating genomic breeding values of threshold traits, and the extended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computing procedures of the three BayesT methods using Markov Chain Monte Carlo (MCMC) algorithm were derived. A simulation study was performed to investigate the benefit of the presented methods in accuracy of genomic estimated breeding values (GEBVs) for threshold traits. Factors affecting the performance of the three BayesT methods were addressed. As expected, the three BayesT methods generally performed better than the corresponding normal Bayesian methods, in particular when the number of phenotypic categories was small. In the standard scenario (No. categories = 2, incidence = 30%, No. QTL = 50, h2 = 0.3), the accuracies were improved by 30.4, 2.4, and 5.7 percentage points, respectively. In most scenarios, BayesTB and BayesTCπ generated similar accuracies and both performed better than BayesTA. In conclusion, our work proved that threshold model fits well for predicting GEBVs of threshold traits, and BayesTCπ is supposed to be the method of choice for genomic selection of threshold traits.