Characterization of dense non-aqueous phase liquid (DNAPL) distribution is important to facilitate the decision of remediation strategies. However, it is still a great challenge to characterize DNAPL source zone architecture with high resolution due to subsurface heterogeneity and relatively sparse data from traditional hydrogeological investigations. To overcome difficulties from such sparse data, electrical resistivity tomography (ERT) is introduced to locate DNAPL using time-lapse cross-borehole measurements. Due to the significant impact of geological heterogeneity on DNAPL source zone architecture, a data assimilation framework based on the coupled multiphase fluids-ERT model is developed to jointly invert DNAPL saturation and the permeability field using time-lapse ERT data. To validate the efficiency and performance of this framework, synthetic and laboratory experiments are both performed to monitor DNAPL migration and distribution in 3D heterogeneous sandbox with cross-borehole ERT. Result shows that time-lapse ERT and direct inversion can map the evolution of the DNAPL plume but loses details regarding the plume morphology due to the over-smoothing caused by geophysical inversion using an isotropic and homogeneous roughness-based regularization procedure. By contrast , the coupled inversion is successful to characterize both the permeability field and the evolution of the DNAPL plume with a higher resolution. This is because the coupled inversion is able to directly translate raw geophysical data into hydrologic meaningful information and therefore avoid artifacts caused by direct geo-physical inversion.