Mandatory regulations in developed countries require that the sulphur content of transportation fuels must drop down to around 15 ppm by now. However, it is difficult to comply with because there is not an efficient method yet to remove thiophene and its derivatives from fuels. A new desulfurization technology with nanoreactions is here presented. Key points of the technology include: 1. A reaction characteristic for sulphur compounds be selected; 2. The reaction is allowed to occur inside pore spaces with nanodimension, where excess of reagents and/or catalyst necessary for the reaction is preloaded. A porous solid with large specific surface area and pore volume provides such spaces and supports the reaction. As consequence, sulphur compounds were completely removed irrespective their dilute concentration of ppm order. Condensation reaction with formaldehyde is effective for the removal of thiophenic compounds, and oxidation reactions are effective for the removal of the remained sulphur compounds. Experiments with model fuels show that thiophene and 4,6-DMDBT were completely removed from different types of fuels, and experiments with commercial diesel and gasoline show that the total sulphur content dropped from hundreds or thousands ppm down to below 15 ppm after treating with the nanoreaction technology while fuel quality was not affected. This technology claims for quite moderate condition, i.e. at ambient pressure and about 70oC; therefore, low operation cost and promising application potential is expected.