The fluorine-modified mesoporous silica HMS(F20) was synthesized by using the mixture of TEFS(SiF(OC2H5)3) and TEOS(Si(OC2H5)4) as the silica source. The specific surface and pore size distribution were characterized by N2 adsorption and the hydrophilic-hydrophobic property was measured by water adsorption. The photocatalytic activities of TiO2 nanoparticles loaded on HMF(F20) and HMS were investigated for the degradation of iso-butanol diluted in water. The results show that the fluorine-modified mesoporous silica HMS(F20) has higher hydrophobic property than HMS and the TiO2/HMS(F20) exhibits the higher photocatalytic activity than TiO2/HMS. The hydrophobic mesopores benefit the condensation of hydrophobic organic compounds diluted in water, which results in higher photocatalytic degradation efficiency.