In order to study the microstructure forming process and modification mechanism of polyacrylate (PA) latex modified mortars during the hardening process, the adsorption performance of PA latex in fresh mortars was analyzed, and the interaction between PA latex and pore solution was simulated. Meanwhile, the microstructure evolution of PA modified mortars was measured by Scanning Electron Microscope (SEM) and Energy Dispersive X-ray Detector (EDX) analysis. The test results show that PA particles chemically react with calcium ions in the pore solution and PA polymer is localized at some places within cement mortar through different morphologies. Based on these experiments, in considering the reactions between PA latex and cement-based materials, an improved polymer modification and microstructure formation model is proposed. This is of great importance for the investigation on the mechanical properties of polymer modified cement-based materials and the application of polymer modified cement-based materials in civil engineering.