The interfacial bonding of the four cellulose nanocrystals (CNCs) and calcium silicate hydrate (C−S−H) in vacuum and solution conditions was analyzed by molecular dynamics simulation. The binding energies were calculated, and the sources of interface strength were analyzed by the formation and lifetime of hydrogen bonds. The adsorption between CNC/ C−S−H was characterized by the movement of interfacial atoms and CNC's adsorption conformation. The types of the functional group determine the bonding of the CNC/C−S−H, and the interface adsorption in two simulation conditions both followed: CNC-C (carboxyl) > CNC-O (hydroxyl) > CNC-N (amino) > CNC-S (sulfonic). The bonding of the interface affects the load transferred between the matrix and CNC, which can be reflected in the overall mechanical properties of the mortar. The mechanical strength of the mortar is in line with the simulation results. CNC-C has the strongest reinforcement effect, while CNC-S has the weakness effect. In the solution simulation, there is almost no chemical adsorption between C−S−H and CNC-S; instead, CNC-S decreased the bonding between the matrix and reduced the strength of the sample. Scanning electron microscopy found that CNC was interspersed in the matrix, riveting the matrix and enhanced the stability of the mortar structure. The influence of CNC on the mortar structure was analyzed by the calcium to silicon ratio (C/S) and it was showed that CNC-C, CNC-O, and CNC-N have an enhancement effect, while CNC-S decreased the coherence of the cement matrix. Durability and nuclear magnetic resonance tests further verified the effect of the four CNCs on the structure of mortar, and results indicated that CNC-C, CNC-O, and CNC-N can control the growth of hydration crystals, fill the cracks, and reduced porosity of samples, while CNC-S reduces the compactness of hydration products and ultimately decreased the mechanical and durability properties of the mortar.