Naphthalene (NAP) is a typical gaseous polycyclic aromatic hydrocarbons (PAHs) pollutant that displays toxicological effects on biosystems. Ordered mesoporous carbon has relatively adequate adsorption capacity; however, the attached hydrophilic functional groups were proven to affect the adsorption performance in the presence of moisture. In this paper, trimethylchlorosilane (TMCS) is used to carry out the hydrophobic modification of ordered mesoporous carbon FDU-15, and the adsorption and desorption properties of FDU-15 were studied. Furthermore, the adsorption isotherms of naphthalene on FDU-15 and modified FDU-15 were fitted by L-F equation, and the kinetic parameters of desorption of naphthalene on modified FDU-15 were analyzed based on the method of temperature programming desorption (TPD). The results showed that the micropore volume and specific surface area of FDU-15 were significantly increased after hydrophobically modified by TMCS, and the polar functional groups of the hydrophobically modified FDU-15 were significantly reduced. Furthermore, the adsorption of naphthalene by FDU-15 before and after modification conformed to the L-F equation (R2 > 99%), and the adsorption of naphthalene by modified FDU-5 at low concentration was significantly improved due to the increase of micropores. Based on desorption kinetic performance study of modified FDU-15, it can be seen that the adsorption kinetic characteristics of naphthalene on the modified FDU-15 conform to the mechanical function of the JMA equation. When the mass ratio of TMCs to FDU-15 is 1:10 in the modification process, the pore structure and surface hydrophobicity of the modified FDU-15 reach an excellent balance. At this time, the adsorbent had the optimum desorption performance under experimental conditions, and the desorption activation energy was decreased from 60.98 kJ/mol of FDU-15 to 50.28 kJ/mol.