Head pose estimation is an important part of gaze tracking but is usually calculated from two-dimensional (2D) images of human faces in most studies. Therefore, a three-dimensional (3D) head pose estimation method of eye tracker based on binocular camera is proposed in this paper. First, the spatial coordinate system and the facial intrinsic coordinate system are established. Then, the facial landmarks of the binocular image are detected by referencing the Dlib and the disparity and 3D coordinates of the corresponding facial landmarks are calculated. Finally, the Euler angle of the 3D head pose is calculated based on the symmetry of the face, and a pitch-angle correction algorithm is applied. To verify the accuracy of the method, a binocular head pose dataset is constructed using model heads and high-precision optical instruments. The experimental results show that the average error of the Euler angle by the method is 1.08° and the root mean square error is 1.25. The accuracy and robustness of the method exceeded those of the OpenFace method based on 2D images.