We investigated the interaction between embedded nanotube and biomembrane using molecular dynamics (MD) simulations. The effects of embedded nanotube on biomembrane were characterized by investigating the influence on the conformational fluctuation of individual lipid molecules, the organization of membrane molecules, the diffusion behavior of lipid molecules, and the diffusion behavior of penetrants inside biomembrane. The steric interaction with the nanotube leads to an entropy reduction of interfacial membrane molecules, while the long-range electrostatic interaction with the N-DWCNT enhances the conformational fluctuation of lipid molecules. The curvature of embedded nanotube could also influence the flexibility of lipid molecules. When the interaction between nanotube and the membrane molecules is weak, the packing density of the membrane is almost unaffected. On the contrary, when the attraction between nanotube and the membrane molecules significantly increases, the attraction among the membrane molecules decreases effectively, which leads to a relaxation of the organization of membrane. With the increase of the strength of electrostatic interaction between nanotube and small polar molecules, interaction-modified friction increases, which leads to the decrease of the diffusion constant of penetrants inside the biomembrane.