Calcium silicate hydrate (C-S-H) is the main hydration product of portland cement. Studying the structural and chemical decomposition of C-S-H after carbonation is critical for determining the durability and serviceability of concrete. Recent studies showed that the mechanical properties are likely to be enhanced when mineral admixtures and polymers are introduced. So far, no molecular-level studies have been conducted on carbonated C-S-H material to clarify these effects. In this research, scanning transmission X-ray microscopy (STXM) is used to study C-S-H modified with two organic polymers (hexadecyltrimethylammonium and polyethylene glycol 200) and exposed to different reaction times with CO2. STXM uses light in the soft X-ray region where a number of atomic resonances are present. By tuning the X-ray energies to a certain absorption edge, elemental and chemical identification was performed. The energy of the X-rays was tuned to the C K-edge, Ca L2,3-edge, and Si K-edge. Detailed images were also recorded with a lateral resolution of 30 nm. Structural, elemental, and chemical heterogeneities were spatially identified. Significant differences were found in carbon spectra in the atmospheric and 48-h continuous CO2-carbonated C-S-H samples, suggesting that carbon-containing precipitates formed within a C-S-H matrix differ depending on the extent of carbonation. Si K-edge spectra suggest increased polymerization of silicates depending on the duration of CO2 exposure. This study found that the degree of silicate polymerization and the coordination environment for carbon-containing mineral phases vary with the CO2 exposure level.