Eye-tracking technology is increasingly used in applications such as 3D displays and human-computer interaction (HCI). However, most current eye trackers focus on 2D point-of-gaze (PoG) estimation and cannot provide accurate gaze depth. Concerning future applications such as HCI with 3D displays, we propose an integrated binocular eye-tracking device with stereo stimuli to provide highly accurate 3D PoG estimation. In our device, the 3D stereo imaging system can provide users with a friendly and immersive 3D visual experience without wearing any accessories. The eye-capturing system can directly record the users’ eye movements under 3D stimuli without disturbance, which can realize front views of eye images while ensuring the user’s wide field of view (FOV). A regression-based 3D eye-tracking model is built based on collected eye movement data under stereo stimuli. Our model estimates users’ 2D gaze with features defined by eye region landmarks and further estimates 3D gaze with a multi-source feature set constructed by comprehensive eye movement features and disparity features from stereo stimuli. Two test stereo scenes with different depths of field are designed to verify the model’s effectiveness. Experimental results of four-fold cross-validation show that the average error for 2D gaze estimation was 0.65°. For 3D gaze estimation, the average errors are 1.69 cm over the workspace volume 50 × 30 × 75 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and 0.14 m over the workspace volume 2.4 × 4.0 × 7.9 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . Two preliminary validation experiments also demonstrate that our system has broad application prospects, such as 3D vision technologies and medical applications related to neurological diseases.