The influenza A M2 channel in the viral envelope is a pH-regulated proton channel that is crucial for viral infection and replication. Amantadine and rimantadine are two M2 inhibitors that have been widely used as anti-influenza drugs. However, due to naturally occurring drug-resistant mutations, their inhibition ability has gradually decreased. These drug-resistant mutations are found at various positions on the transmembrane domain of the M2 protein and could be categorized to three types: mutations close to the drug-binding site located at the pore-facing positions (V27A, A30T, S31N, and G34E); mutations at the interhelical interfaces at the N-terminal half of the channel (L26F); and mutations outside the drug-binding site lying at the interhelical interfaces (L38F, D44A). Investigating the structures and the M2-inhibitor interactions of these mutants would illuminate drug inhibition and drug resistance mechanisms and guide the design of novel anti influenza drugs targeting these drug-resistant mutants. In this study, we chose four mutations at different positions (V27A, S31N, L26F, L38F) and conducted molecular dynamics simulations on both the apo-form and the drug-bound forms. The protein structures as well as the water structure in the channel pore were analyzed. Stable water clusters facilitating drug binding were found. Both the protein pore radius profiles and the structure of the water clusters were sensitive to the mutations. Based on our simulations, we compared the structures of the mutated proteins and proposed possible mechanisms for drug resistance of these mutations.