The success of deep learning is largely attributed to the training over clean data. However, data is often coupled with noisy labels in practice. Learning with noisy labels is challenging because the performance of the deep neural networks (DNN) drastically degenerates, due to confirmation bias caused by the network memorization over noisy labels. To alleviate that, a recent prominent direction is on sample selection, which retrieves clean data samples from noisy samples, so as to enhance the model’s robustness and tolerance to noisy labels. In this paper, we revamp the sample selection from the perspective of optimal transport theory and propose a novel method, called the OT-Filter. The OT-Filter provides geometrically meaningful distances and preserves distribution patterns to measure the data discrepancy, thus alleviating the confirmation bias. Extensive experiments on benchmarks, such as Clothing1M and ANIMAL-10N, show that the performance of the OT- Filter outperforms its counterparts. Meanwhile, results on benchmarks with synthetic labels, such as CIFAR-10/100, show the superiority of the OT-Filter in handling data labels of high noise.