Extreme environment and complex load conditions put forward higher requirements for the material properties of concrete. The method of improving concrete performance by modifying cement-based material with polymer has been widely used. To reveal the hardening mechanism of the hydration process of epoxy latexes-modified cementitious materials, the influence of epoxy latexes on the hydration process of cement hydration was studied by isothermal calorimetry, and the phase evolution of the cement clinker minerals and hydration products was tracked by in-situ XRD. The results show that the retardation effect of epoxy latexes on cement hydration is related to the interaction among epoxy particles, cement clinker minerals and hydration products, and the interaction effect becomes more obvious with time-dependent. When epoxy latexes are added into the cement paste, the heat-generation rate slows down, and the heat flow peak and cumulative heat generation reduce. Epoxy latexes can delay silicate reaction and aluminate reaction by inhibiting the dissolution of cement minerals (C3S, C3A and gypsum) and the precipitation of hydration products (ettringite and portlandite). The effect of epoxy latexes on cement hydration increases with the increase of its content.