Accurate measurement of the microcirculation dynamics, including the blood vessel 3D structure, blood flow velocity and the blood flow transit time can not only improve our understanding of the pathology of microcirculation dysfunction-related disease, but also provide important parameters for disease diagnosis, prevention, and early treatment. In this work, we introduce a comprehensive optical coherence tomography (OCT)-based functional imaging technology for the 3D measurement of the micro vessel networks' structure, blood flow velocity, and the blood flow transit time. The M-mode data acquisition (repeated A-scans) was employed in this technique. For blood vessel 3D structure imaging, we developed a first order field autocorrelation function (g1)-based adaptive analysis method to suppress the blood vessel tail artifacts and enhance the blood flow in small vessels. For blood flow velocity 3D imaging, we developed a set of quantitative dynamic analysis methods to measure both the axial and total blood flow velocity of the complex vessel network. We further developed a graphing method to obtain the 3D topological parameters of the 3D vessel network, including the vessel skeleton, branching, vessel diameter, and the blood flow speed at each location. With those information, we are able to, to the best of our knowledge, obtain the 3D blood transit time in the complex vessel network for the first of time. The proposed technique has the advantage of obtaining these three important blood flow biomarkers from a single data acquisition, which greatly simplifies the experiment procedure. The proposed OCT approach has a wide application in the field of microcirculation dysfunction-related disease studies.