Vigilance state is crucial for the effective performance of users in brain-computer interface (BCI) systems. Most vigilance estimation methods rely on a large amount of labeled data to train a satisfactory model for the specific subject, which limits the practical application of the methods. This study aimed to build a reliable vigilance estimation method using a small amount of unlabeled calibration data. We conducted a vigilance experiment in the designed BCI-based cursor-control task. Electroencephalogram (EEG) signals of eighteen participants were recorded in two sessions on two different days. And, we proposed a contrastive fine-grained domain adaptation network (CFGDAN) for vigilance estimation. Here, an adaptive graph convolution network (GCN) was built to project the EEG data of different domains into a common space. The fine-grained feature alignment mechanism was designed to weight and align the feature distributions across domains at the EEG channel level, and the contrastive information preservation module was developed to preserve the useful target-specific information during the feature alignment. The experimental results show that the proposed CFGDAN outperforms the compared methods in our BCI vigilance dataset and SEED-VIG dataset. Moreover, the visualization results demonstrate the efficacy of the designed feature alignment mechanisms. These results indicate the effectiveness of our method for vigilance estimation. Our study is helpful for reducing calibration efforts and promoting the practical application potential of vigilance estimation methods.