The invention relates to a process of naphtha desulphurization. The process comprises devices of a sedimentation tank and a desulphurization reactor, wherein size of the sedimentation tank is 2-3 times of that of the desulphurization reactor, a bottom of the sedimentation tank is provided with a draining valve; the desulphurization reactor is a fixed-bed desulphurization reactor, a bottom of the desulphurization reactor is filled with molecular sieves or ceramic ball inert substances, a desulfurizer is filled in the molecular sieves or the ceramic ball inert substances, a filled height of the molecular sieves or the ceramic ball inert substances is 1/10-1/3 of a filled height of the desulfurizer, and the bottom of the desulphurization reactor is provided with a draining valve. The naphtha is put into the sedimentation tank for sedimentation and dehydration, water generated in the sedimentation tank is discharged from the draining valve at the bottom, the dehydrated naphtha is put into the fixed-bed desulphurization reactor for desulphurization reaction, and water gathered at the bottom of the desulphurization reactor is discharged from the draining valve arranged at the bottom of the desulphurization reactor. The method can prevent damages of the water in the naphtha and the water generated during the reaction on desulfurizer strength, and thus the desulfurizer can be continuously used for more than one year.