Alkali-activated cementitious material is a new type of low-carbon material. The pore solution of alkali-activated cementitious materials generally has more alkalinity than cement-based materials, inevitably leading to the different volume deformation caused by alkali-aggregate reaction. Granite was selected as a representative aggregate to prepare alkali-activated metakaolin-slag mortar for exploring the relationship between the alkalinity of pore solution and alkali-aggregate reaction. The deformation behaviors of mortar immersed in the NaOH solution with different concentrations were studied. According to the microstructure analysis, it is shown that the volume shrinkage of alkali-activated cementitious materials can effectively suppress the expansion caused by alkali-aggregate reaction. Under different soaking conditions, the alkali-activated metakaolin-slag mortar exhibits different deformation behaviors. The expansion behavior of alkali-activated metakaolin-slag mortar is caused by the alkali-aggregate reaction products and the transformation from a zeolite-like structure sodium silicaluminate hydrate gel to a zeolite structure gel. Alkali-aggregate reaction would occur when the hydroxyl ion concentration in the pore solution of alkali-activated cementitious materials is greater than 0.209 mol/L.