Relative permeability curves are one of the crucial factors that control the behavior of multiphase flow in petroleum reservoirs. Accurate prediction of the relative permeability curve involving emulsification and emulsion transport in emulsion flooding is vital to enhancing heavy oil recovery. In this study, a relative permeability characterization model including the emulsification mechanism and emulsion transport is developed, in which residual oil saturation and end-point permeability for water are parametrized as functions of emulsion concentration and capillary number. Based on the built characterization model, an inversion method (ensemble Kalman filter) is used to estimate the relative permeability curves of emulsion flooding. The inversion results of four sets of emulsion flooding experiments show that the errors of end points between the Johnson−Bossler−Neumann method and inversion method are less than 10%. For the continuous emulsification process in the in situ emulsion flooding tests, the inversed relative permeability curves shift between the upper and the inferior limits of the permeability. The error of residual oil saturation between the inversion and the experiment is less than 10%. In summary, this study demonstrates the feasibility of using the characterization model and inversion method to infer the relative permeability curves of emulsion flooding, which can aid in the predictions of multiphase flow in heavy oil reservoirs.