Currently, a novel shrinkage-reducing polycarboxylate superplasticizer (SR-PCA) is used to control cementitious shrinkage. To clarify its mechanism when applied in cementitious materials, the influence of SR-PCA on the composition, morphology, and structure of synthetic calcium-silicate-hydrate (C-S-H), together with the interaction between SR-PCA and C-S-H at the atomic level, is investigated. For comparison, a commercial polycarboxylate superplasticizer (PCA) is also employed. The results show PCA and SR-PCA can adsorb on the C-S-H surface rather than intercalate into the layers. Compared with PCA, SR-PCA has a milder impact on C-S-H crystallinity. SR-PCA refines the pore structure of C-S-H drastically, whereas PCA loosens the structure by increasing the mesopore volume. In addition, the adsorption effect of SR-PCA on the C-S-H surface is less significant than that of PCA. At the atomic level, this less adsorption of SR-PCA is attributed to the lower adhesion energy of the C-S-H/SR-PCA interface due to the weaker Ca-O bond strength.