Given that CO chamber and high inner pressure are needed in the traditional carbonation curing, we propose an in-situ internal carbonation by mesoporous silica nanoparticles (MSN) to tackle the challenge, leveraging its high specific surface area. In this study, MSN was functionalized with γ-aminopropyl triethoxy silane (MSN-amine), followed by reacting with CO (CO carrier) and mixing with alite paste. Phase transformation and nucleation behavior were investigated by conducting comparative in-situ carbonation of alite paste, utilizing MSN-amine in two configurations: one adsorbing CO (MSN-amine-AC) and the other desorbing CO (MSN-amine-DC). Results indicated that semi-crystalline C-S-H is produced in alite paste containing MSN-amine-DC (Ap-MSN-DC) through pozzolanic reaction while amorphous calcium carbonate (ACC) is generated in alite paste with MSN-amine-AC (Ap-MSN-AC) via in-situ carbonation, both of which promote the early reaction of alite. Additionally, low Ca/Si ratio calcium silicate hydrate (C-S-H) with negative electric potential developed as MSN-amine-DC gradually eroded, collapsed, and chemically transformed into reactive sites. Conversely, the ACC generated in MSN-amine-AC blocks the mesopores, inhibits the pozzolanic reaction and preserves the silica skeleton. Subsequently, calcite is crystallized via the dissolved ACC and embedded itself on the surface of C-S-H with positive electric potential, turning to nucleation sites physically. To conclude, the proposed in-situ internal carbonation models for MSN-amine-modified alite paste offer insights into microstructural evolution.