Conformal prediction for time series presents two key challenges: (1) leveraging sequential correlations in features and non-conformity scores and (2) handling multi-dimensional outcomes. We propose a novel conformal prediction method to address these two key challenges by integrating Transformer and Normalizing Flow. Specifically, the Transformer encodes the historical context of time series, and normalizing flow learns the transformation from the base distribution to the distribution of non-conformity scores conditioned on the encoded historical context. This enables the construction of prediction regions by transforming samples from the base distribution using the learned conditional flow. We ensure the marginal coverage by defining the prediction regions as sets in the transformed space that correspond to a predefined probability mass in the base distribution. The model is trained end-to-end by Flow Matching, avoiding the need for computationally intensive numerical solutions of ordinary differential equations. We demonstrate that our proposed method achieves smaller prediction regions compared to the baselines while satisfying the desired coverage through comprehensive experiments using simulated and real-world time series datasets.