Mixup, a simple data augmentation method that randomly mixes two data points via linear interpolation, has been extensively applied in various deep learning applications to gain better generalization. However, its theoretical explanation remains largely unclear. In this work, we aim to seek a fundamental understanding of the benefits of Mixup. We first show that Mixup using different linear interpolation parameters for features and labels can still achieve similar performance as standard Mixup. This indicates that the intuitive linearity explanation in Zhang et al., (2018) may not fully explain the success of Mixup. Then, we perform a theoretical study of Mixup from the feature learning perspective. We consider a feature-noise data model and show that Mixup training can effectively learn the rare features (appearing in a small fraction of data) from its mixture with the common features (appearing in a large fraction of data). In contrast, standard training can only learn the common features but fails to learn the rare features, thus suffering from bad generalization performance. Moreover, our theoretical analysis also shows that the benefits of Mixup for feature learning are mostly gained in the early training phase, based on which we propose to apply early stopping in Mixup. Experimental results verify our theoretical findings and demonstrate the effectiveness of the early-stopped Mixup training.