We propose a Doppler optical micro-angiography (DOMAG) method to image flow velocities of the blood flowing in functional vessels within microcirculatory tissue beds in vivo. The method takes the advantages of recently developed optical micro-angiography (OMAG) technology, in which the endogenous optical signals backscattered from the moving blood cells are isolated from those originated from the tissue background, i.e., the tissue microstructures. The phase difference between adjacent A scans of OMAG flow signals is used to evaluate the flow velocity, similar to phase-resolved Doppler optical coherence tomography (PRDOCT). To meet the requirement of correlation between adjacent A scans in using the phase resolved technique to evaluate flow velocity, an ideal tissue-sample background (i.e., optically homogeneous tissue sample) is digitally reconstructed to replace the signals that represent the heterogeneous features of the static sample that are rejected in the OMAG flow images. Because of the ideal optical-homogeneous sample, DOMAG is free from the characteristic texture pattern noise due to the heterogeneous property of sample, leading to dramatic improvement of the imaging performance. A series of phantom flow experiments are performed to evaluate quantitatively the improved imaging performance. We then conduct in vivo experiments on a mouse brain to demonstrate that DOMAG is capable of quantifying the flow velocities within cerebrovascular network, down to capillary level resolution. Finally, we compare the in vivo imaging performance of DOMAG with that of PRDOCT, and show that DOMAG delivers at least 15-fold increase over the PRDOCT method in terms of the lower limit of flow velocity that can be detected.