Boron nitride (BN) nanosheet is a novel material with great potential in biomedical applications. A deep understanding of the basic interaction mechanisms between biosystems and foreign BN nanosheets can help to better clarify the potential risks of these nanomaterials and provide guidance on their safe design. In this paper, we show that BN nanosheets can cause degradation of bacterial cell membranes via experimental and simulation-based approaches. Our extensive molecular dynamics simulations results reveal that BN nanosheets cause toxicity to both bacterial outer and inner membranes in which hydrophobic effect plays an important role. The spontaneous lipid extraction by BN nanosheets is in agreement with the free-energy calculations. A liquid-to-gel phase transition is induced by the BN nanosheet in the outer model membrane of bacteria, indicating that the BN nanosheet may cause higher toxicity to the outer membrane than to the inner membrane. Our findings may offer new insights into the molecular basis of BN's cytotoxicity and antibacterial activity.