Accurate prediction of dynamical systems in unstructured meshes has recently shown successes in scientific simulations. Many dynamical systems have a nonnegligible level of stochasticity introduced by various factors (e.g. chaoticity), so there is a need for a unified framework that captures both deterministic and stochastic components in the rollouts of these systems. Inspired by regeneration learning, we propose a new model that combines generative and sequential networks to model dynamical systems. Specifically, we use an autoencoder to learn compact representations of full-space physical variables in a low-dimensional space. We then integrate a transformer with a conditional normalizing flow model to model the temporal sequence of latent representations. We evaluate the new model in both deterministic and stochastic systems. The model outperforms several competitive baseline models and makes more accurate predictions of deterministic systems. Its own prediction error is also reflected in its uncertainty estimations. When predicting stochastic systems, the proposed model generates high-quality rollout samples. The mean and variance of these samples well match the statistics of samples computed from expensive numerical simulations.