The generalizable face anti-spoofing (FAS) has attracted much attention recently. Even though many existing methods perform well under intra-domain settings, the model’s performance in the unseen domain is not satisfying. In this paper, we shift our attention to the frequency domain to seek a solution. Specifically, we examine the characteristics of different frequency band components of FAS images and observe that the model’s cross-domain performance is very sensitive to low-frequency features. To alleviate this sensitivity and improve the model’s performance in FAS cross-domain tasks, we propose a new approach called Masked Frequency Autoencoders (MFAE). MFAE randomly masks a portion of frequencies on the low-frequency spectrum of the image and then reconstructs the image from the resulting embedding. This innovative Masked Image Modeling (MIM) strategy can be used as a self-supervised task for pre-training vision transformers (ViTs), which can reduce the ViT encoder’s sensitivity to domain shifts. Additionally, we add an auxiliary content-regularization decoder in our MFAE to encourage the encoder to be insensitive to low-frequency features. The results show that the model insensitive to low-frequency features performs well on extensive public datasets and outperforms other state-of-the-art methods in cross-domain FAS tasks.