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This paper explores the effects of cone tip roughness factor, soil in situ stress ratio and strength non-homogeneity on cone tip resistance in three-layer clay deposits, aiming at presenting a general CPT data interpretation framework to extract soil layered profiles and strengths. Large deformation finite element (LDFE) analysis has been carried out, simulating continuous penetration of the standard cone penetrometer from the seabed surface, with the consideration of cone tip roughness factor, in situ stress ratio and soil strength non-homogeneity within a practical range. In the LDFE analyses, a thin relatively stiff or soft clay layer was interbedded in a uniform or NC clay deposit, with various strength ratios between two successive layers and thickness ratios of the thin layer to the cone diameter explored.The results have shown that the noted factors have significant influence on net cone penetration resistance in stratified deposits. These influences in the layered deposits were found to be similar in magnitude to those on the cone limiting resistance in a single clay layer, leading to the resultant influence on a thin layer correction factor for cone penetration resistance minimal. This was confirmed by the evidence of the evolving soil flow mechanisms around the cone tip. Therefore, the design charts and formulas developed for a smooth cone in uniform three-layer soils are applicable for delineating layer boundaries and interpreting the undrained shear strength of each identified layer for a partially rough cone in three-layer non-homogeneous clay deposits. However, the cone tip roughness factor was shown to have an influence in the layer boundary identification, especially for the cone penetration from a stiff layer to a soft layer. © 2017 Elsevier B.V.