The invention provides a method and a system for testing the entering depth of a stratified oil deposit profile control water plugging agent. The method comprises the following steps: step 1, establishing a cross flow anisotropic physical simulation model by virtue of a plugging agent distribution law physical simulation method, and obtaining a physical simulation result by use of cross flow anisotropic physical simulation model; step 2, establishing a numerical simulation model by virtue of a plugging agent distribution law numerical simulation method, drawing a relative permeability curve of plugging agents with different displacement velocities, and modifying the numerical simulation model by use of the relative permeability curve of the plugging agents so as to obtain a numerical simulation result; step 3, analyzing the planar distribution law and longitudinal distribution law of the plugging agent under different injection pressures by virtue of comprehensively utilizing the fit physical simulation result and the numerical simulation result; establishing a scaled model of the plugging agent entering into a cross flow region and an non-cross flow region according to the analysis result; step 4, establishing a plugging agent dosage optimization method of the stratified oil deposit profile control water plugging agent by utilizing the scaled model of the plugging agent entering into the cross flow region and the non-cross flow region.