The transport properties of water molecules in nanochannels are critical to the durability of porous materials. In this article, molecular dynamics simulations are used to study the effects of poly(acrylic acid) (PAA), poly(vinyl alcohol) (PAA), and poly(ethylene glycol) (PEG) on the durability of modified cement-based materials. By establishing ideal composite nanopores, the absorption of water molecules in the channel is simulated. The results show that PEG has the best water-blocking effect under the same simulated conditions, followed by PVA, and PAA is the most unfavorable. This difference in the water-blocking effect can be explained by two factors. On the one hand, hydrophobic alkane groups in these polymers can inhibit water molecule transport. A large number of -COOH and -OH functional groups in PAA and PVA will form a complex H-bond network with the water molecules in the nanopore, dragging the water molecules forward, thereby speeding up the water molecule transmission to a certain extent. However, PEG, which mainly contains low-polar oxygen (C-O-C), has weak hydrogen bonding with water molecules, so the water-blocking effect is more obvious. On the other hand, the van der Waals interaction and the electrostatic interaction mainly derived from Op-Caw-Os can ensure the absorption of the polymer on the C-S-H surface during the transport process. The -COOH in PAA ensures its strongest absorption. But PVA and PEG will morphologically agglomerate during the water absorption, occupying pores and hindering the transport of water molecules.