We present a computationally efficient framework, called FlowDRO, for solving flow-based distributionally robust optimization (DRO) problems with Wasserstein uncertainty sets while aiming to find continuous worst-case distribution (also called the Least Favorable Distribution, LFD) and sample from it. The requirement for LFD to be continuous is so that the algorithm can be scalable to problems with larger sample sizes and achieve better generalization capability for the induced robust algorithms. To tackle the computationally challenging infinitely dimensional optimization problem, we leverage flow-based models and continuous-time invertible transport maps between the data distribution and the target distribution and develop a Wasserstein proximal gradient flow type algorithm. In theory, we establish the equivalence of the solution by optimal transport map to the original formulation, as well as the dual form of the problem through Wasserstein calculus and Brenier theorem. In practice, we parameterize the transport maps by a sequence of neural networks progressively trained in blocks by gradient descent. We demonstrate its usage in adversarial learning, distributionally robust hypothesis testing, and a new mechanism for data-driven distribution perturbation differential privacy, where the proposed method gives strong empirical performance on high-dimensional real data.