The Lindqvist anion [Mo₆O₁₉]²⁻ was in situ intercalated into layered double hydroxides (LDHs) via a one-pot hydrothermal method. The heterogeneous catalyst was applied in ultra-deep desulfurization of fuels under mild conditions, and exhibited high activity for dibenzothiophene (DBT), benzothiophene (BT) and 4,6-dimethyldibenzothiophene (4,6-DMDBT). The above sulfur-containing compounds could be completely transformed into their corresponding sulfones under the stoichiometric O/S molar ratio (O/S molar ratio = 2). Furthermore, the catalyst could be easily recovered and reused at least 7 times without an obvious decrease in performance. The possible desulfurization mechanism was also studied in detail.