Ultrahigh-resolution optical coherence Doppler tomography (lODT) demonstrates great potential for quantitative blood flow imaging owing to its large field of view and capillary resolution. However, lODT only detects the axial flow velocity and requires Doppler angle correction to retrieve the absolute velocity. Although methods for Doppler angle tracking of single or few large vessels have been reported, a method that enables angle correction of the entire 3D microvascular networks remains a challenge. Here, we present a method based on eigenvalue analysis of 3D Hessian matrix to retrieve the orientation of each tubular vessel. As the algorithm is voxel based, it is suitable for effective tracking of Doppler angle matrix and restoring the absolute flow over the 3D vascular flow networks. We present results on simulation and flow phantom studies to show its efficacy for accurate 3D angle tracking and absolute flow correction. Then, we perform an in vivo validation study on mouse micro-circulatory cerebral blood flow (CBF) networks, which clearly demonstrates the capability of this method for tracking the Doppler angle matrix of the highly complex 3D CBF networks. Published by AIP Publishing. [http://dx.doi.org/10.1063/1.4973367] Ultrahigh-resolution optical coherence Doppler tomography (lODT) has been shown to enable determination of 3D cerebral blood flow velocity (CBFv) of mouse brain capillary networks over a large field of view (FOV). 1 Owing to its intrinsic Doppler effect induced by the red blood cell velocity (v RBC ), lODT detects the apparent v RBC , i.e., the averaged axial component v z of v RBC by calculating the accumulative phase shift between two successive A-scans. 2