The invention specifically provides a modified IM-5 molecular sieve and a preparation method and application thereof, belonging to the field of modification of molecular sieves. The modified IM-5 molecular sieve has a mesoporous area of 150 m<2> / g or above and a mesoporous volume of 0.5 cm<3> / g or above. The modified IM-5 molecular sieve has a large mesoporous area and a large mesoporous volume, so a reactant can more easily contact with an acid center and a product can be rapidly diffused from active center to places out of a catalyst; thus, side reactions are prevented, and the activity, selectivity and service life of the catalyst are improved; e.g., when the modified IM-5 molecular sieve is applied to an alkylation reaction of benzene and methanol, the catalyst has the advantages of a slow inactivation rate, a high benzene conversion rate and high target product selectivity. The modified IM-5 molecular sieve can be used under a high space velocity condition, has high catalysis efficiency, is reactable at a low temperature, shows good activity stability, reduces energy consumption of alkylation, prolongs the service life of the catalyst and is suitable for industrial application.