Abstract Incorporation of corrosion inhibitor into the cement-slag composite pastes can effectively improve the resistance to seawater erosion. However, corrosion inhibitor inevitably affects the microstructures and transport properties of cement-slag composite pastes, which poses a great challenge for the engineering application prospects of the composite pastes modified by corrosion inhibitor. In this paper, a smart organic polymer with hydrophilic and hydrophobic components is designed as corrosion inhibitors, and a combination of experiments and molecular dynamics (MD) simulations is employed to investigate the effect of this smart polymer-based corrosion inhibitor on cement-slag composite pastes under seawater erosion. Experiments show that this smart polymer-based corrosion inhibitor has profound effect on the hydration properties, pore structures and ions resistance of cement-slag composite pastes, with an optimum content of approximately 6%. MD simulations reveal the nano-mechanism by which this smart polymer-based corrosion inhibitor hinders water and ion transport in the calcium aluminate-silicate hydrate (CASH) nanopores. Analysis suggests that strong electrostatic interactions, originating from the CaCASH-Oinhibitor pairs and the H-bond networks, are the primary sources of the corrosion inhibitor-CASH bonding mechanism. Besides, the migration rates of water and ions are reduced as the large cluster structures formed among the corrosion inhibitor molecules, water molecules and erosive ions.