Alkali activated materials (AAMs) have received worldwide attention due to its lower embodied energy and environmental impact than that of traditional cementitious materials. However, the activators with high alkalinity may raise the risk of alkali silica reaction (ASR) induced deterioration when reactive aggregates are used, which thereby limits the commercial use of AAMs. Not speaking the ASR induced long-term expansion, the early-age reaction of AAMs prepared with reactive aggregates is largely unknown. In this paper, isothermal calorimetry, thermogravimetry (TG) and mercury intrusion porosimetry (MIP) were adopted to study the heat evolution, mineralogical changes and pore structures of early-age ordinary Portland cement (OPC) mortar and water-glass activated slag/fly ash mortars. In each system, emphasis were made to understand the differences between mixtures prepared with standard inert quartz sands and reactive fine aggregates. The results show that the mortars prepared with reactive aggregates generated more heat in the wetting and dissolution stage. Particularly, the water-glass activated slag mortar presented the highest heat flow peak. Meanwhile, the results of TG illustrate that higher amount of reaction products were formed in water-glass activated mortars prepared with reactive aggregates than that with inert quartz sands. These findings suggest that the reactive aggregates are evidently involved in the early-age alkaline reaction of AAMs system.