The development of carbon-based nanomaterials has extensively facilitated new discoveries in various fields. Carbon nanotube-based nanocomposites (CNT-based nanocomposites) have lately recognized as promising biomaterials for a wide range of biomedical applications due to their unique electronic, mechanical, and biological properties. Nanocomposite materials such as silver nanoparticles, polymers, biomolecules, enzymes, and peptides have been reported in many studies, possess a broad range of antibacterial activity when incorporated with carbon nanotubes (CNTs). It is crucial to understand the mechanism which governs the antimicrobial activity of these CNT-based nanocomposite materials, including the decoupling individual and synergistic effects on the cells. In this review, the interaction behavior between microorganisms and different types of CNT-based nanocomposites is summarized to understand the respective antimicrobial performance in different conditions. Besides, the current development stage of CNT-based nanocomposite materials, the technical challenges faced, and the exceptional prospect of implementing potential antimicrobial CNT-based nanocomposite materials are also discussed.