Facial expression is among the most natural methods for human beings to convey their emotional information in daily life. Although the neural mechanism of facial expression has been extensively studied employing lab-controlled images and a small number of lab-controlled video stimuli, how the human brain processes natural facial expressions still needs to be investigated. To our knowledge, this type of data specifically on large number of natural facial expression videos is currently missing. We describe here the natural Facial Expressions Dataset (NFED), a fMRI dataset including responses to 1,320 short (3-second) natural facial expression video clips. These video clips is annotated with three types of labels: emotion, gender, and ethnicity, along with accompanying metadata. We validate that the dataset has good quality within and across participants and, notably, can capture temporal and spatial stimuli features. NFED provides researchers with fMRI data for understanding of the visual processing of large number of natural facial expression videos.