In this study, three fluoroalkyl trimethoxysilanes (FATMS) with different chain length of fluoroalkyl moiety, i.e., (3,3,3-trifluoropropyl) trimethoxysilane (C1), (1,1,2,2-tetrahydro-nonafluorohexyl) trimethoxysilane (C4), (1,1,2,2-tetrahydro-perfluorooctyl) trimethoxysilane (C6), were incorporated into component A of a two-component polyurethane (2K PU) clearcoat to assure their chemical anchoring with polymer chains, and then cured with polyisocyanate hardener. The hydrophobic durability of FATMS-modified coatings was further examined under various service conditions by water contact angle analyzer, attenuated total reflection Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and element-mapping. Hydrophobic 2K PU clearcoats could be achieved at FATMS dosage below 5.0 %, 0.5 %, and 0.5 % for C1, C4, and C6 additive, respectively. All coatings maintained their original hydrophobicity after for two years’ ambient storage, immersing in ambient water or mere UV irradiation. But if UV irradiation and/or heat (i.e., high-temperature) were imposed together with water, the coatings would quickly lose their surface hydrophobicity due to the loss of fluoroalkyl groups via hydrolysis break of Si-O-C chemical bond. The UV irradiation-induced synergistic effect on failure of surface hydrophobicity should be resulted from the increased hydrophilicity of PU matrix, which enhanced the affinity of water molecules with the coatings and hence higher hydrolysis probability of Si-O-C bond. Therefore, FATMS route is more suitable for fabrication of hydrophobic 2K PU clearcoats used indoors at room temperature.