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Existing optical flow estimators usually employ the network architectures typically designed for image classification as the encoder to extract per-pixel features. However, due to the natural difference between the tasks, the architectures designed for image classification may be sub-optimal for flow estimation. To address this issue, we propose a neural architecture search method named FlowNAS to automatically find the better encoder architecture for flow estimation task. We first design a suitable search space including various convolutional operators and construct a weight-sharing super-network for efficiently evaluating the candidate architectures. Then, for better training the super-network, we propose Feature Alignment Distillation, which utilizes a well-trained flow estimator to guide the training of super-network. Finally, a resource-constrained evolutionary algorithm is exploited to find an optimal architecture (i.e., sub-network). Experimental results show that the discovered architecture with the weights inherited from the super-network achieves 4.67\% F1-all error on KITTI, an 8.4\% reduction of RAFT baseline, surpassing state-of-the-art handcrafted models GMA and AGFlow, while reducing the model complexity and latency. The source code and trained models will be released in https://github.com/VDIGPKU/FlowNAS.