The removal of thiophene sulfides was considered as one of the major steps for producing clean diesel fuel. We prepared a defect-rich Pr/Ce–N–TiO2 for breaking carbon-sulfur bonds of thiophene sulfides aided by visible light. Prepared photocatalysts of Pr/Ce–N–TiO2-2 had a large specific surface area of 114 m2/g and a pore diameter of 20–30 nm. The experimental results displayed the Turnover Frequency of thiophene, benzothiophene, dibenzothiophene, and 4, 6-dimethyl-dibenzothiophene was 50, 48, 45, and 49, respectively. Interestingly, the proper content of defects on the surface distinctly improved the activity of the oxidation and in situ hydrogenation of dibenzothiophenes. And desulfurization ratios were 100% when the composition of Pr3+, Ce3+, Ti3+, and Oads on the surface of the catalyst was 10.6, 6.6, 18.9, and 12.3%. The consequences of Photoluminescence emission spectra, Ultraviolet and visible spectrophotometry, and Electron paramagnetic resonance spectroscopy showed the co-doping of N, Pr, and Ce extended the photo-absorption range and increased the hole-electron separation of TiO2, which might be because the synergy of N, Pr, and Ce increased oxygen vacancies and defects on the catalytic surface, and formed lower gap energy leading to transfer and reserve electrons quickly under visible light. Also, we speculated the mechanism of photocatalytic desulfurization over Pr/Ce–N–TiO2 depending on the experimental results.