Determining　the　amine　molecules　behaviors　in　the　nanochannels　enables　the　interpretation　of　the　microstructure　and　macroscopic　properties　of　amines　modified　cement　based　materials.　In　this　study,　quantitative　analysis　were　performed　on　the　behaviors　of　amine　molecules　(TEPAs,　PAMs　and　TEAs)　by　molecular　dynamics　(MD)　simulation　in　the　nanochannels　of　C–S–H　gel.　According　to　the　interaction　of　amine　molecules　with　C–S–H　gel　substrates　or　water　molecules,　research　works　revealed　that　amine　molecules　with　special　spatial　structures　illustrate　different　aggregation　behaviors.　TEPAs　with　linear　structures　tend　to　aggregate　in　a　regular　sequence　at　the　center　of　the　C–S–H　gel　nanochannels.　Instead,　PAMs　and　TEAs　with　branched　structures　prefer　dispersing　in　the　aqueous　solution　in　the　C–S–H　gel　nanochannels.　Such　different　aggregation　behaviors　allow　amine　molecules　to　have　various　penetration　depth　and　residence　time　in　the　interfacial　regions.　It　was　found　that　oxygen　atoms　and　active　hydrogen　atoms　in　PAMs　and　TEAs　can　form　stable　interaction　with　calcium　ions　and　oxygen　atoms　of　C–S–H　gel　substrates,　respectively.　The　oxygen　involved　bonds　are　stronger　than　nitrogen　involved　ones　for　all　the　molecules　due　to　great　electronegativity.　There　is　no　formation　of　hydrogen　bonds　in　TEPAs,　but　polar　atoms　in　PAMs　and　TEAs　can　interact　through　hydrogen　bonding.　Moreover,　TEPAs　cannot　form　strong　hydrogen　bonding　with　water　molecules　due　to　their　aggregation　behavior,　whereas　PAMs　and　TEAs　formed　strong　hydrogen　bonding　with　surrounding　water　molecules.　In　addition,　formation　of　more　hydrogen　bonding　with　amine　molecules　leads　to　a　lower　diffusion　coefficient　of　water　molecules.　Breakage　of　hydrogen　bonds　of　water　molecules　causes　the　final　failure　of　C–S–H/amine　molecules　nanocomposites　subjected　to　tensile　loads.　©　2021