An effective process to remove sulfur compounds from fuel has been explored. The tungsten atoms modified MoO3 as active species was used to enhance the desulfurization activities, and MOF materials to provide a stable place. Meanwhile, the successful introduction of magnetic Fe3O4 could lead to an easily separation after the reaction with simple external magnet to achieve the catalyst recycling use and the final catalyst was named as Fe3O4@W-MoO3@MOF. To noted, various W contents in catalyst system showed a different influence on the ODS process and the ultra-deep desulfurization result could be obtained once the 30 % W loading amount was introduced. Under the optimal reaction conditions, DBT could be completely oxidized in 60 min and there is no apparent losing of activity after at least 18 times of recycling. As for the actual diesel, it was demonstrated that an excellent reactivity was also achieved.