Pathological changes of penetrating arteries (PAs) may be an important contributing factor of cerebral small vessel disease (SVD). Measurement of PA flow velocity and diameter with phase contrast (PC) MRI remains challenging due to the presence of strong partial volume effects. Here we propose model-based analysis of complex difference (MBAC) images to quantify diameter and velocity of PAs. We demonstrated the accuracy of the MBAC method with simulation and phantom studies. In vivo PA diameter and velocity were obtained for the first time. The MBAC method may serve as a useful tool for understanding the etiopathogenesis of SVD.