This experimental study examined the aplication effect of polycaprolactone (PCL), an organic resin material with excellent elasticity and ductility, on improving the mechanical performance of cellulose nanocrystal (CNC) cement composites. PCL was compared according to its shape, and in the case of Granules, which is the basic shape, interfacial adhesion with cement was not achieved, so a dichloromethane (DCM) solution was used to dissolve and use the Granules form. As a method for bonding PCL to the CNC surface, the CNC surface was modified using 3-aminopropyltriethoxysilane (APTES), and surface silylation was confirmed through Fourier transform infrared spectroscopy (FT-IR) analysis. In order to evaluate the dispersibility according to the application of PCL to the modified CNC, particle size analysis (PSA) and zeta potential analysis were performed according to the PCL mixing ratio. Through the PSA and zeta potential values, the highest dispersion stability was shown at 1 vol.%, the cohesive force of CNC was low, and the dispersion stability was high according to the application of PCL. According to the results of the dispersion stability evaluation, the degree of hydration of the dissolved PCL 1 vol.%, CNC-only specimens, and plain specimens were analyzed. CNC acted as a water channel inside the cement to accelerate hydration in the non-hydrated area, resulting in an increased degree of hydration. However, the incorporation of PCL showed a low degree of hydration, and the analysis of strength characteristics also showed a decrease of approximately 27% compared with that of plain specimens. This was because the bonding with SiO2 was not smooth owing to the solvent, thus affecting internal hydration. In order to investigate the effect of the PCL shape, the compressive and flexural strength characteristics were compared using PCL powder as an additional parameter. The compressive strength and flexural strength were improved by about 54% and 26%, respectively, in the PCL powder 15 wt% specimen compared to the general specimen. Scanning electron microscopy (SEM) analysis confirmed that the filler effect, which made the microporous structure denser, affects the mechanical performance improvement.