The morphological identification and molecular dimension estimation of organochlorine compounds (OCCs) in two different naphtha samples were performed. The analysis result of gas chromatography equipped with an electron capture detector indicates that the chloroaromatics are predominant OCCs in the two naphtha samples, and a small amount of chloroolefins and chloroalkanes coexisted with them. The main OCCs (>3 mg/L) in naphtha I are 1,2⁃dichlorobenzene, 1,4⁃dichlorobenzene, 1,6⁃dichlorohexane, 1,1⁃dichloroethylene, 2⁃chloroethylbenzene and 1,2⁃dichloropropane, and that in naphtha II are 1,2⁃dichloropropane and 1,4⁃dichlorobenzene. The three⁃dimensional dimension of 14 identified OCCs are determined by softwares, whose minimum cross⁃sectional diameter is between 0.4 nm and 1.0 nm by further estimation. The high abundance of OCCs, which easily are converted to corrosive hydrogen chloride and ammonium chloride during processing, in naphtha may be a primary cause of increased malfunction in naphtha prehydrogenation unit. The porous adsorption material with micropore close to the molecular diameter is beneficial for the adsorption removal of OCCs.