This paper describes a numerical study on soil characterization of stiff over soft clays in centrifuge test using cone penetration test (CPT), especially when the top stiff layer is thin relative to the centrifuge cone size. An extensive parametric study was conducted using large deformation finite element (LDFE) analysis, with the cone penetrating continuously from the soil surface. The LDFE model has been validated against existing physical test data with very good agreement. Since the bottom soft clay was normally thick enough to fully mobilise the ultimate cone resistance, its undrained shear strength can be interpreted by the existing approach for cone deep penetration in a uniform clay layer. Thus, the challenge was to interpret the strength of the top stiff layer, where the layer thickness was not thick enough to fully mobilise its ultimate resistance. Both top layer thickness ratios (to the cone diameter) and layer strength ratios were considered in the parametric study. Based on the results from LDFE analyses, the interpretation formula of the undrained shear strength in the top stiff layer was proposed as a set of new bearing factors. The proposed cone bearing factor was a function of the ratio of the measured peak cone resistance in the top layer to the stable/ultimate cone resistance in the bottom layer and the ratio between the top layer thickness to the cone diameter. The formula can be used directly when the top layer thickness was known based on the sample preparation. However, the layer interface can be identified based on the study here, if the top layer thickness was not certain. A design flow chart was provided for interpretations of top clay layer strength and top layer thickness based on the cone resistance profile obtained from CPT test.