Cementitious composites incorporating well-dispersed carbon nanotubes (CNTs) have demonstrated significant mechanical performance enhancements, however, there has only been limited investigation into the nanocomposite microstructure and pore structure. In this study, the effects of (i) CNT dispersion with and without the assistance of a dispersant, (ii) CNT dose at 0.05–0.25 wt% of cement, and (iii) CNT dispersion quality upon the composite microstructure after 7- and 28-days' hydration were investigated using quantitative image analysis of backscattered electron microscopy and X-ray computed microtomographic datasets. Results show that dispersed CNTs promoted the formation of low- and higher-density hydration products within 7 days of hydration and reduced the pore size distribution by 28 days, although 3D X-ray results showed some large CNT agglomerations formed in the nanocomposite. Further, poorly-dispersed CNTs increased the 28-day pore size distribution, but had a beneficial effect, similar to well-dispersed CNTs, upon the microstructural composition of the hydrated phases.