A novel nanofluidic impact protection system is introduced in this paper, consisting of hydrophobic heterojunction carbon nanotubes (HCNTs) and water molecules. When the capillary resistance of the nanopores is overcome, water molecules can infiltrate into nanopores such as to convert external impact energy into excessive surface energy. A model of a single HCNT with water molecules in a reservoir is established and validated. The effects of several dominant parameters (e.g., nanopore size, impact velocity) are evaluated, and the potential mechanism is illustrated. The effect of the carbon nanotube structure on the nanofluidic behavior of the HCNT-water system is investigated. Results reveal that the segment of carbon nanotubes close to the water reservoir determines the energy absorption efficiency of the system.