The interaction between mechanical wave initiated by impact load and nanoporous energy absorption system (NEAS) is investigated using molecular dynamics (MD) simulations, which includes the forward procedure (stage I) and the reflected procedure (stage II) of mechanical wave. The current NEAS is made of one-end closed single-walled carbon nanotubes (CNTs) and water. The effects of impact loading rate and tube size on the energy absorption of NEAS are also considered. After the bulk water is pushed into CNTs by the impact load, a new water interface will be created. The water molecules on interface have a much higher potential energy than their bulk counterpart, and this energy change can be defined as liquid interfacial energy, which gives the main contribution to the energy absorption of NEAS. As compared to stage I, the liquid interfacial energy density at stage II is significantly increased, especially for smaller tubes with a higher loading rate, and thus stage II can provide the significant contribution to the system energy absorption and must be considered in the energy absorption procedure. In addition, when water transports through CNTs, the solid–liquid friction based on the ven der Waals (VDW) interaction between CNTs and water is very small because the VDW repulse force can be partially canceled by the VDW attraction force, and the net force is very small; thus, the contribution of the solid–liquid friction to the energy absorption of NEAS can be neglected.