Particulate methane monooxygenase (PMMO) is an membrane-bound metalloenzyme that catalyses the biological conversion of alkane to alcohol. The study on the binding modes between alkane and the catalytic mechanism of PMMO may aid the design of a new synthetic catalyst, which uses alkane as an alternative new energy source. The binding modes of PMMO with a series of alkanes were obtained via molecular docking method, then two 6 ns molecular dynamics simulations were performed for both PMMO and PMMO-pentane complex systems. Finally, conformation cluster and binding energy analysis were implemented for the complex systems. The results show that pentane binds to the hydrophobic pocket near the zinc ion, which is comprised by three segments (i.e., the residues from M45 to W60, R190 to T193 in pmoA subunit and Q161 in pmoC subunit). Compared with PMMO, PMMO-pentane complex maintains a similar motive mode but a more remarkable motive extent. Additionally, large-scale motion of pentane in the hydrophobic pocket is important for the catalysis of PMMO. The results of binding energy computations still revealed that the stable recognition of PMMO by pentane was mainly driven by the hydrophobic interactions. All the simulation results agree well with experimental data.