Vascular Doppler optical coherence tomography (DOCT) images with weak boundaries are usually difficult for most algorithms to segment. We propose a modified random walk (MRW) algorithm with a novel regularization for the segmentation of DOCT vessel images. Based on MRW, we perform automatic boundary detection of the vascular wall from intensity images and boundary extraction of the blood flowing region from Doppler phase images. Dice, sensitivity, and specificity coefficients were adopted to verify the segmentation performance. The experimental study on DOCT images of the mouse femoral artery showed the effectiveness of our proposed method, yielding three-dimensional visualization and quantitative evaluation of the vessel.