We report the use of an electrically tunable lens (ETL) in a 1.3 μm spectral-domain optical coherence tomography (SD-OCT) system to overcome the depth of focus (DOF) limitation in conventional OCT systems for OCT angiography (OCTA) in a mouse cerebral cortex. The ETL provides fast and dynamic control of the axial focus of the probe beam along the entire range of the mouse cortex, upon which we performed cerebral blood flow imaging of all cortical layers by stitching the OCTA images automatically captured at six focal depths. Capillary vasculature and axial blood flow velocity were revealed in distinctive cortical layers and, for the first time, to the best of our knowledge, in white matter. The results have shown the system capability to conveniently investigate the hemodynamics in deep cortical layers in the mouse brain. More importantly, the compact integration of an ETL will benefit the future design of handheld or intra-cavity OCT probes for a wide range of applications in research and clinical fields.