Density functional theory was used to study monomolecular cracking reaction of n-butane on acidic zeolite. Geometry optimizations of the local structures of the species reacting with the zeolite were carried out by using the 5T cluster model at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level. In this work, the deprotonation modes of two different order C atoms in n-butane cracking on H-ZSM-5 were explored in detail by the density functional theory. The calculated activation barriers at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level are 238 kJ/mol for the primary C-C cracking, 217 kJ/mol for the secondary C-C cracking, 296 kJ/mol for the primary dehydrogenation, and 242 kJ/mol for the secondary dehydrogenation, respectively. The difference of the activation barrier is 54 kJ/mol for the deprotonation reactions of two different order C atoms in n-butane. For the dehydrogenation reaction, the results indicate that the reaction is expected to be preferred at the secondary C atom. Additionally, the relation between the acidity and structure of the cluster shows that the acidity effect of the zeolite can be simulated by modifying the peripheral bonds of the cluster for the 5T cluster. Finally, the zeolite acidity effects on the reaction barriers were investigated by changing the cluster terminal Si-H bond length.