A fundamental understanding of the interactions between one-dimensional nanomaterials and the cell membrane is of great importance for assessing the hazardous effects of viruses and improving the performance of drug delivery. Here, we propose a finite element-based coarse-grained model to describe the cell entry of nanomaterials based on an absolute nodal coordinate formula and Brownian dynamics. The interactions between nanoparticles and lipid membrane are described by the Lennard–Jones potential, and a contact detection algorithm is used to determine the contact region. Compared with the theoretical and published experimental results, the correctness of the model has been verified. We take two examples to test the robustness of the model: the endocytosis of nanorods grafted with polymer chains and simultaneous entry of multiple nanorods into a lipid membrane. It shows that the model can not only capture the effect of ligand–receptor binding on the penetration but also accurately characterize the cooperative or separate entry of multiple nanorods. This coarse-grained model is computationally highly efficient and will be powerful in combination with molecular dynamics simulations to provide an understanding of cell–nanomaterial interactions.