The photocatalytic oxidative desulfurization is one of the promising processes to realize the deep desulfurization of the fuel. A series of TiO2 nanoparticles (TiO2 NPs) were prepared to investigate the effect of annealing temperatures on its physical properties and the photocatalytic oxidative desulfurization performance. Their physicochemical properties were investigated by X–ray diffraction (XRD), fourier transform infrared spectroscopy (FTIR), thermal gravimetric and differential thermal analysis (TG–DTA), scanning electron microscopy (SEM), and X–ray energy dispersive spectrometer (EDS). The results show that, the crystallite structure of TiO2 NPs annealed at 250–450°C was mainly composed of anatase phase. The rutile phase appeared when the anneal temperature increased to 550°C and all of the anatase converted into rutile phase when annealed at 750°C. The effect of crystallite structure of TiO2 on its photocatalytic oxidative desulfurization performance was investigated using benzothiophene (BT) as the model sulfur compound. The anatase phase was preferable for the photocatalytic oxidation of BT. Phase transfer catalyst plays an important role for improving the photocatalytic desulfurization rate. The photocatalytic oxidative reaction mechanism was also proposed in the presence of TiO2 as catalyst, H2O2 as oxidant, and the DMDAAC as phase transfer catalyst. In the heterogeneous catalytic system, the entire reaction rate is mainly determined by the oxidation reaction and the extraction process, in which the oxidation process could be the rate determining step.