To understand catalytic cracking processes of alkanes in the petrochemical industry, the monomolecular cracking mechanism of n-hexane in the H-FAU zeolite has been examined using ab initio molecular dynamics simulations combined with enhanced sampling techniques. It has been found that the adsorption energies of short n-alkanes are linearly correlated with the chain length and contact areas with the zeolite framework, while no such correlation can be applied to the short n-alkenes. High-dimensional free energy landscapes characterizing four cracking modes of n-hexane at three different temperatures have been drawn. The electron transfer in the cracking process was analyzed by quantifying the charge evolution for carbon atoms. The formation of carbonium ions in each cracking mode is found to be the rate-limiting step. At high temperature, free energy differences are nonpositive values, suggesting that the cracking of n-hexane is spontaneous, which is also coincident with the experimental observation. The cracking of the central C–C bond of n-hexane is easier than the cracking of terminal C–C bonds, which is due to the lower free energy barrier. The present work sheds new insights into the cracking process of n-alkanes in the industrially used FAU zeolite catalysts.