Magnetic resonance (MR) imaging of microvascular flow is an important topic in biomedicine because it permits access to the functional state of a biologic system. The internal heterogeneous magnetic field due to susceptibility differences within tissues is one of the factors that can affect signal intensity. A glass bead phantom simulating a porous medium was used to experimentally study the effect of the internal magnetic field on MR flow measurements. A physical model was developed to simulate the paths of the moving spins and the local magnetic field distribution in the medium to estimate the signal intensity with spin-phase analysis. The susceptibility variation inside the glass bead phantom was estimated by comparing the simulation results with the experimental data. Experiments were also performed with a tissue-simulating phantom, and the results indicated that the effect of the internal field inhomogeneity on in vivo microvascular flow measurements was negligible.