The microstructure forming process of polyacrylate (PA) latex modified cement-based materials was investigated from mixing to hardening. Owing to the chemical reaction between PA particles and calcium ions in the pore solution, PA polymer will not uniformly disperse in cement mortar due to its adsorption on cement particles or hydrates. As a result, PA polymer should exist in cement mortars through different morphologies. The early age mechanical properties of PA modified mortars are lower than those of unmodified mortars, while a rapid progress of the compressive strength and fracture energy can be recognized from the PA modified mortars. It was found that PA polymer addition will refine the small pores but induce big pores to cement mortar. SEM and EDX analysis proves that PA polymer is localized at some places within PA modified mortar which can be named as the localization of polymer modification. The physical and chemical influence of PA polymer on cement-based materials was integrated into an improved model. © 2013 Elsevier Ltd. All rights reserved.