Augmented reality-based brain–computer interface (AR–BCI) has a low signal-to-noise ratio (SNR) and high real-time requirements. Classical machine learning algorithms that improve the recognition accuracy through multiple averaging significantly affect the information transfer rate (ITR) of the AR–SSVEP system. In this study, a fast recognition method based on a separable convolutional neural network (SepCNN) was developed for an AR-based P300 component (AR–P300). SepCNN achieved single extraction of AR–P300 features and improved the recognition speed. A nine-target AR–P300 single-stimulus paradigm was designed to be administered with AR holographic glasses to verify the effectiveness of SepCNN. Compared with four classical algorithms, SepCNN significantly improved the average target recognition accuracy (81.1%) and information transmission rate (57.90 bits/min) of AR–P300 single extraction. SepCNN with single extraction also attained better results than classical algorithms with multiple averaging.