In cement-based materials, the microstructure evolution is a key factor that determines the mechanical, rheological and transport properties. However, the principal mechanism of microstructure evolution becomes more complicated due to the incorporation of limestone powder. In this paper, the effects of limestone powder are divided into filling effect, dilution effect, nucleation effect and its negative feedback effect. The hydration of paste is controlled by the nucleation and dilution effects, while the microstructure evolution of paste is determined by the nucleation, dilution and filling effects of limestone powder. Based on this, the HYMOSTRUC model was used to investigate the effect of content and specific surface area of limestone powder on microstructure evolution. In order to reveal the mechanism of microstructure evolution, a model of evolution of interparticle force is developed, in which the transition between the force of cementitious particles and the C-S-H cohesion is determined by cement hydration. By applying the model, the relationship between microstructure evolution and interparticle force was established, and the effect of limestone powder on microstructure evolution can be divided into five stages on the time scale depending on the action mechanism of interparticle forces.