The use of supplementary cementitious materials (SCMs) around the world to improve concrete performance has increased in recent decades. However, the application of SCMs remains limited by their heterogeneity and variability. Engineering practices demand a unified model for SCMs to predict and optimise the performance of blended concrete. A multiphase modelling scheme that covers various SCMs is therefore proposed in this study. Following this modelling scheme, three low-calcium fly ashes were selected and comprehensively studied by scanning electron microscopy–energy dispersive X-ray spectroscopy (SEM-EDS) full-element mapping and image analysis. The pozzolanic reactivity of these three fly ashes was further investigated in alkaline and cement systems. A temperature-dependent two-phase pozzolanic reaction model (silicate and Al-silicate glass) considering fly ash material variations was proposed to predict the pozzolanic reaction and therefore the degree of reaction at different temperatures. The numerical results show that the proposed multiphase modelling scheme has great potential to cover various SCMs.