The interaction of two-dimensional (2D) nanomaterials and bacterial membranes has attracted tremendous attention in antibacterial applications. Various peculiarities of 2D nanomaterials may lead to multiple mechanisms of their interactions with membranes. Here, we investigated the interaction between molybdenum disulfide (MoS2) nanosheets and the bacterial membrane by using both theoretical and experimental approaches. Molecular dynamics simulation presented that MoS2 nanosheets can disrupt the structure of the lipid membrane by making dents on its surface and extracting phospholipid molecules to reduce the integrity of the membrane. This is attributed to the combination of the dispersion interaction of lipid tails with S atoms and the electrostatic interactions of lipid head groups with the Mo and S atoms in the lateral edges of the MoS2 nanosheet. Scanning electron microscopy and transmission electron microscopy confirmed the dents and the destruction of the cell membrane, which would lead to the loss of cytoplasm and the death of bacteria. It should be noted that the phenomenon where MoS2 induces a dent is different from the direct insertion of graphene-based nanomaterials, which might be due to the thicker and stiffer structure of MoS2. Therefore, we believe that the molecular interactions of 2D nanomaterials with bacterial membranes should be highly correlated with their structural characteristics. This newly discovered mechanism of MoS2 nanomaterials to disrupt the cell membrane may promote the application of transition metal dichalcogenide (TMD) nanomaterials in designing remarkable antibacterial materials in the near future.