Due to the limited pixel pitch of the spatial light modulator (SLM), the field of view (FOV) is insufficient to meet binocular observation needs. Here, an optimized controlling light method of a binocular holographic three-dimensional (3D) display system based on the holographic optical element (HOE) is proposed. The synthetic phase-only hologram uploaded onto the SLM is generated with the layer-based angular spectrum diffraction theory, and two different reference waves are introduced to separate the left view and the right view of the 3D scene. The HOE with directional controlling light parameters is employed to guide binocular information into the left-eye and the right-eye viewing zones simultaneously. Optical experiments verify that the proposed system can achieve binocular holographic augmented reality 3D effect successfully with real physical depth, which can eliminate the accommodation-vergence conflict and visual fatigue problem. For each perspective, the FOV is 8.7° when the focal length of the HOE is 10 cm. The width of the viewing zone is 2.3 cm when the viewing distance is 25 cm.