Isomorphously substituted LTL zeolite ([M]-LTL) was studied by the periodic density functional theory. Two different tetrahedral Si atoms of LTL (T1 and T2) were replaced by a series of trivalent atoms (M=Al, B and Ga). The relative energies of the different structural configurations show that the T1 site located at the 12-membered rings is the most favorable site for M substitution. For the [M]-LTL where T1 is substituted, different Brønsted acid sites (O3, O4, and O6) were intensively studied by calculating the deprotonation energy, the O–H vibrational frequency, and the charge of the bridging oxygen, and the adsorption energy of the probe molecules (ethylene, acetonitrile and pyridine) with the [B]-, [Ga]-, and [Al]-LTL models. A direct correlation between those four parameters is observed and the trend of the relative Brønsted acidity for isomorphously substituted systems is predicted as: [B]-LTL<<[Ga]-LTL<[Al]-LTL which is in agreement with the experimental sequence of isomorphously substituted ZSM-5 zeolite.