This paper is the second part of an overall research project that aims to model the hydration kinetics of composite cementitious materials. The new hydration kinetic model of Portland cement was constructed in the first part of this research project. The aim of this part is to characterize the physical effect of SCMs by modifying some kinetic parameters of the hydration kinetic model of cement. In this paper, the filler effect of SCMs is attributed to the "dilution effect", "nucleation effect" and "accelerated dissolution effect". The dilution effect is considered by introducing the actual water/cement ratio into the kinetic model. The nucleation surface area, nucleation and growth rates are modified to account for the nucleation effect and accelerated dissolution effect of fillers. The simulative fit results show that the extra contribution of SCMs due to their filler effect on hydration of cement at early ages has an upper limit: at most 20% extra nucleation surface area, 30% extra nucleation ratio and 40% extra growth ratio of calcium silicate hydrate (CSH). The new modified kinetic model and the value-taking method of the newly introduced parameters are verified by simulative fitting to the kinetic data from reference. The apparent activation energies of the nucleation rate, growth rate, and diffusion rate are approximately 35 kJ/mol, 36 kJ/mol and 38.5 kJ/mol, which are slightly smaller than those of the pure Portland cement reported in the first part of this research project.