To offer better guidance to the physical simulation experiment scheme and model parameters design of water flooding in low permeability carbonate reservoirs，the similarity theory on the oil-water two-phase seepage simulation was analyzed further. Starting from seepage theory of deformation media，mathematical model of nonlinear flow for dual porosity media was established considering variation regularity of stress sensitivity of permeability and starting pressure gradient.The similarity criteria of physical water flooding simulation in the low permeability carbonate reservoir was deduced by analytic equation method. The dimensionless equation was solved using IMPES method，and the principal and subordinate relations of various similarity criteria were determined quantitatively by distortion and sensitivity analysis，which were verified by the results of stress sensitivity experiment and water flooding experiment. Results show that this model veritably represents the regularity of water flooding in the low permeability carbonate reservoir. Twenty-one similarity criteria have various effects on objective function. When the model and prototype are not completely similar in the physical simulation design，the permeability and saturation of the porous medium and the viscosity and density of multiphase fluids should be given priority，as well as the pore structure similarity.