AmtB is one of the ammonium transporter proteins facilitating the ammonium transport across the cellular membranes. Experimentally, the substrate used in in vitro studies is the radio labeled [(14)C]methylammonium, rather than ammonium itself. To explore the similarity and difference of the conduction mechanism of methylamine and ammonia molecules through AmtB, molecular dynamics simulations on 22 carefully designed systems were performed, which demonstrated that methylamine could be automatically transported in a very similar way to ammonia. The driving force for the conduction is mainly the hydrogen bond network comprising His168, His318, and Tyr32, working in coordination with NH-π interaction with residue Trp212. Then, Ser263 translocated the substrates from the exit gate into the cytoplasm by hydrogen bond interaction. The aromatic ring of Trp212 acted like a springboard to facilitate the translocation of the substrates from site Am2 to Am4 via NH-π interaction. Without the mediation of Trp212, further movement of substrate in the channel would be hampered by the strong hydrogen bonding from His168. In agreement with experimental results, the substrates could be transported by W212F mutant but not by W212A within the simulation time as long as 20 ns. In addition, we predicted that the mutants S263D and S263C remain the function of the transporter but S263A does not. The difference of transporting the two substrates is that methylamine involves more hydrophobic interactions than ammonia. In conclusion, methylamine molecule is a good mimic for investigating the translocation mechanism of ammonium transporter AmtB.