In this work, we analyze the characterization of drainage multiphase flow properties on heterogeneous rock cores using a rich experimental data set and mm‐m scale numerical simulations. Along with routine multiphase flow properties, 3‐D submeter scale capillary pressure heterogeneity is characterized by combining experimental observations and numerical calibration, resulting in a 3‐D numerical model of the rock core. The uniqueness and predictive capability of the numerical models are evaluated by accurately predicting the experimentally measured relative permeability of N2—DI water and CO2—brine systems in two distinct sandstone rock cores across multiple fractional flow regimes and total flow rates. The numerical models are used to derive equivalent relative permeabilities, which are upscaled functions incorporating the effects of submeter scale capillary pressure. The functions are obtained across capillary numbers which span four orders of magnitude, representative of the range of flow regimes that occur in subsurface CO2 injection. Removal of experimental boundary artifacts allows the derivation of equivalent functions which are characteristic of the continuous subsurface. We also demonstrate how heterogeneities can be reorientated and restructured to efficiently estimate flow properties in rock orientations differing from the original core sample. This analysis shows how combined experimental and numerical characterization of rock samples can be used to derive equivalent flow properties from heterogeneous rocks.