Abstract: Objective For the system of two single-walled carbon nanotubes (CNTs) placed in parallel onto a cell membrane, we investigate the effect of the interaction between carbon nanotubes on the wrapping manner of carbon tubes by the membrane, and obtain the energy-optimized configurations. Methods We develop a physical model for membrane-wrapped CNTs considering the interaction between two CNTs, and introduce parameters describing the morphology of the cell membrane and positions of CNTs. The Helfrich model based on continuum mechanics is used to calculate the membrane’s bending energy and the Lennard-Jones potential is introduced to describe the interaction between CNTs. We obtain the free energy of the system at different distances of NTs by the look-up table method, and the typical configurations of the system. Results Compared to the case wherein the interaction between CNTs is not considered, the free energy profile of the system significantly changed: the deep well appears on the energy curve at a distance between CNTs of carbon ~0.3 times the tube diameter; as the distance between CNTs increases, the energy returns to the case wherein the interaction between CNTs is not considered. Conclusions Under the consideration of the interaction between CNTs, we find that the wrapping manner of CNTs by the cell membrane is changed, and the two CNTs tend to contact during their endocytosis. This work may be helpful in understanding and developing novel nanotube-based system for drug delivery.