Objective. Accurately diagnosing patients with disorders of consciousness (DOC) is challenging and prone to errors. Recent studies have demonstrated that EEG (electroencephalography), a non-invasive technique of recording the spontaneous electrical activity of brains, offers valuable insights for DOC diagnosis. However, some challenges remain: (1) the EEG signals have not been fully used; and (2) the data scale in most existing studies is limited. In this study, our goal is to differentiate between minimally conscious state (MCS) and unresponsive wakefulness syndrome (UWS) using resting-state EEG signals, by proposing a new deep learning framework. Approach. We propose DOCTer, an end-to-end framework for DOC diagnosis based on EEG. It extracts multiple pertinent features from the raw EEG signals, including time-frequency features and microstates. Meanwhile, it takes clinical characteristics of patients into account, and then combines all the features together for the diagnosis. To evaluate its effectiveness, we collect a large-scale dataset containing 409 resting-state EEG recordings from 128 UWS and 187 MCS cases. Main results. Evaluated on our dataset, DOCTer achieves the state-of-the-art performance, compared to other methods. The temporal/spectral features contributes the most to the diagnosis task. The cerebral integrity is important for detecting the consciousness level. Meanwhile, we investigate the influence of different EEG collection duration and number of channels, in order to help make the appropriate choices for clinics. Significance. The DOCTer framework significantly improves the accuracy of DOC diagnosis, helpful for developing appropriate treatment programs. Findings derived from the large-scale dataset provide valuable insights for clinics.