Holographic near-eye displays (NEDs) offer a promising pathway toward compact and immersive virtual and augmented reality (VR/AR) systems by enabling natural 3D perception through wavefront reconstruction. Although advances in computational algorithms have improved image quality and real-time performance, practical implementations of holographic NEDs still face challenges in achieving high-quality reconstruction and apparent depth cues without bulky optics. In this Letter, we propose what we believe to be a novel multi-aperture pupil optimization algorithm tailored for lensless holographic NEDs that enhances reconstructed image quality and depth perception. The method is validated through simulations and optical experiments.