Adaptive optics (AO) based ophthalmic imagers, such as scanning laser ophthalmoscopes (SLO) and optical coherence tomography (OCT), are used to evaluate the structure and function of the retina with high contrast and resolution. Fixational eye movements during a raster-scanned image acquisition lead to intra-frame and intra-volume distortion, resulting in an inaccurate reproduction of the underlying retinal structure. For three-dimensional (3D) AO-OCT, segmentation-based and 3D correlation based registration methods have been applied to correct eye motion and achieve a high signal-to-noise ratio registered volume. This involves first selecting a reference volume, either manually or automatically, and registering the image/volume stream against the reference using correlation methods. However, even within the chosen reference volume, involuntary eye motion persists and affects the accuracy with which the 3D retinal structure is finally rendered. In this article, we introduced reference volume distortion correction for AO-OCT using 3D correlation based registration and demonstrate a significant improvement in registration performance via a few metrics. Conceptually, the general paradigm follows that developed previously for intra-frame distortion correction for 2D raster-scanned images, as in an AOSLO, but extended here across all three spatial dimensions via 3D correlation analyses. We performed a frequency analysis of eye motion traces before and after intra-volume correction and revealed how periodic artifacts in eye motion estimates are effectively reduced upon correction. Further, we quantified how the intra-volume distortions and periodic artifacts in the eye motion traces, in general, decrease with increasing AO-OCT acquisition speed. Overall, 3D correlation based registration with intra-volume correction significantly improved the visualization of retinal structure and estimation of fixational eye movements.