Alite (impure C3S) being the major and most reactive phase in ordinary portland cement has been studied extensively. This paper focuses on the mathematical modeling of new hypothesis developed, densified volumetric growth, applied to the main hydration peak in alite hydration. This hypothesis assumes a time and particle size-dependent growth rate and densification rate of C-S-H controlled by its internal surface area. To test this hypothesis, a new microstructural modeling platform (Cementitious Reactions Simulator) has been developed. The model was used to calibrate and predict the isothermal calorimetric results from the literature and two sets of original experimental results with alite replaced with different replacement fractions of quartz, fly ash, and slag of different fineness. The model is able to capture and predict the effect of fineness and fillers without the need of varying the parameters for the particular set of simulations. The values of the parameters of simulation reflect the current experimental evidence from the literature and thus provide validation of the hypothesis which suggests that the main hydration period including deceleration period in the alite hydration is induced by the densification and reducing outer growth rate of C-S-H.