In this study, multi-walled nanotubes (MWCNTs) functionalized with carboxyl group are used as additives with different morphologies of chiral, zigzag and armchair to investigate the effects of three MWCNTs on the mechanical and water absorption properties of cement-based composites. Accordingly, two different concentrations of 0.05 and 0.1 wt.% of MWCNTs are incorporated in the cement paste with a water-to-cement ratio of 0.4. The results indicate that the chiral sample for 0.05 wt.% at the age of 7 and 28 days and 0.1 wt.% at 7 days, and the armchair sample with 0.1 wt.% at the age of 28 days have the highest compressive strength. The flexural strength at 7 and 28 days show that the chiral MWCNT composite has the greatest increase in strength for both 0.05 and 0.1%. The ranking of water absorption is chiral < zigzag < armchair < PC and armchair < chiral < zigzag < PC for 0.05 and 0.1 wt.% MWCNT at 28 days, respectively. The results, thus, show that the lowest percentage of water absorption is obtained by 0.05% chiral MWCNT-COOH and 0.1% armchair MWCNT-COOH at the age of 28 days. The effect of bridging, connecting MWCNTs and hydration products provided by MWCNTs-COOH, is, thus, confirmed by SEM.