The present research is focused on the investigation of the influence of ultrafine additives on the structure formation of hardened cement paste and the establishment of the mechanisms of the morphological transformations, which determine the properties of hydrated products. In the course of the research, the modification of ordinary Portland cement was performed by the suspension of multi-walled carbon nanotubes (MWCNTs), carbon black (CB) paste, and silica fume (SF). Scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) microanalysis, X-ray diffraction (XRD) analysis, thermal analysis, and Fourier-transform infrared (FTIR) spectroscopy were used to study cement hydration products. The morphology of hardened cement paste depends on the chemical reactivity of additives, their geometry, and their genesis. The action mechanism of the inert carbon-based additives and pozzolanic silica fume were considered. The cement hydration products formed in the process of modification by both types of ultrafine additives are described. In the case of the modification of cement paste by inert MWCNTs and CB paste, the formation of cement hydration products on their surface without strong adhesion was observed, whereas in the case of the addition of SF separately and together with MWCNTs, the strong adhesion of additives and cement hydration products was noted.