Driving facial animation based on tens of tracked markers is a challenging task due to the complex topology and to the non-rigid nature of human faces. We propose a solution named manifold Bayesian regression. First a novel distance metric, the geodesic manifold distance, is introduced to replace the Euclidean distance. The problem of facial animation can be formulated as a sparse warping kernels regression problem, in which the geodesic manifold distance is used for modelling the topology and discontinuities of the face models. The geodesic manifold distance can be adopted in traditional regression methods, e.g. radial basis functions without much tuning. We put facial animation into the framework of Bayesian regression. Bayesian approaches provide an elegant way of dealing with noise and uncertainty. After the covariance matrix is properly modulated, Hybrid Monte Carlo is used to approximate the integration of probabilities and get deformation results. The experimental results showed that our algorithm can robustly produce facial animation with large motions and complex face models. Driving facial animation based on tens of tracked markers is a challenging task due to the complex topology and to the non-rigid nature of human faces. We propose a solution named manifold Bayesian regression. First a novel distance metric, the geodesic manifold distance, is introduced to replace the Euclidean distance. The problem of facial animation can be formulated as a sparse warping kernels regression problem, in which the geodesic manifold distance is used for modeling the topology and discontinuities of the face models. The geodesic manifold distance can be adopted in Traditional regression methods, eg radial basis functions without many modulated. We put facial animation into the framework of Bayesian regression. approximate the integration of probabilities and get deformation results. The experimental results showed that our algorithm can robustly produce facial animation with large motions and complex face models.