Multi-wall carbon nanotubes (CNTs) and natural organic matters (NOMs) were chosen as target pollutants in this study. The effects of CNTs on the formation of disinfection by-products during chlorination of different types of NOMs (Suwannee river standard humic acid (HASR) and Suwannee river standard fulvic acid (FASR)) were investigated. Compared with the single system of CNTs or NOMs, the presence of CNTs increased the yields and initial formation rates of trihalomethanes (THMs) and halogenated acetic acids (HAAs) in the binary systems. Both CNTs and NOMs could serve as precursors of disinfection by-products, leading to more active sites for chlorination in NOMs-CNTs system. Therefore, the yields and initial formation rates of binary systems increased. Moreover, the initial formation rate of THMs and HAAs formed by HASR were higher than those formed by FASR in the absence and presence of CNTs. This was due to the higher aromaticity of HASR than FASR, which favored the attack of hypochlorous acid. In addition, the adsorption amount of HASR to CNTs was greater than FASR, which resulted in its stronger effects on the formation of disinfection by-products than FASR.