This study investigated the effects of organic polymers (polyethylene glycol and hexadecyltrimethylammonium) on structures of calcium silicate hydrates (C-S-H) which is the major product of Portland cement hydration. Increased surface areas and expansion of layers were observed for all organic polymer modified C-S-H. The results from attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopic measurements also suggest lowered water contents in the layered structures for the C-S-H samples that are modified by organic polymers. Scanning transmission X-ray microscopy (STXM) results further supports this observation. We also observed difference in the extent of C-S-H carbonation due to the presence of organic polymers. No calcite formed in the presence of HDTMA whereas formation of calcite was observed with C-S-H sample modified with PEG. We suggest that the difference in the carbonation reaction is possibly due to the ease of penetration and diffusion of the CO(2). This observation suggests that CO(2) reaction strongly depends on the presence of organic polymers and the types of organic polymers incorporated within the C-S-H structure. This is the first comprehensive study using STXM to quantitatively characterize the level of heterogeneity in cementitious materials at high spatial and spectral resolutions. The results from BET, XRD, ATR-FTIR, and STXM measurements are consistent and suggest that C-S-H layer structures are significantly modified due to the presence of organic polymers, and that the chemical composition and structural differences among the organic polymers determine the extent of the changes in the C-S-H nanostructures as well as the extent of carbonation reaction.