Objective For the system of two single-walled carbon nanotubes (CNTs) placed in parallel onto a cell membrane, effects of the interaction between carbon nanotubes on wrapping manner of carbon tubes by the membrane were investigated, and the energy-optimized configurations were obtained. Methods A physical model for membrane-wrapped CNTs considering the interaction between two CNTs, and parameters describing the morphology of cell membrane and positions of CNTs were introduced. The Helfrich model based on continuum mechanics was used to calculate the membrane’s bending energy and the Lennard-Jones potential was introduced to describe the interaction between CNTs. Free energy of the system at different distances of NTs was calculated by the look-up table method, and the typical configurations of the membrane-wrapped CNTs was obtained. Results Compared with the case wherein the interaction between CNTs was not considered, the free energy profile of the system significantly changed. Deep well appeared on energy curve, when the distance between CNTs of carbon was 0.3 times of the tube diameter; as the distance between CNTs increased, the energy returned to the case wherein the interaction between CNTs was not considered. Conclusions With introduction of the interaction between CNTs, the wrapping manner of CNTs by the cell membrane changed, and the two CNTs tended to contact during their endocytosis. These results provide theoretical references for understanding and developing novel nanotube-based system for drug delivery.