The effects of calcium on the atomic structure of alkali-activated binder materials were investigated. The alkali-activated binder samples with varied Ca/Si ratios were first statically examined with both the X-ray diffraction (XRD) and total scattering function analysis. The added calcium can reorder the atomic structure of the alkali-activated materials and enhance its crystallization based on the X-ray pair distribution function (PDF) and XRD analysis. In situ PDF experiments were undertaken to examine the evolution of the atomic structure of calcium-contained geopolymer. The increase in calcium content accelerated the dissolution of precursor and the formation of the binder. It was shown that the additional Ca(OH)(2) could serve as nucleation sites for the precipitation of sodium aluminosilicate hydrate gel to accelerate the reaction. PDF analysis and XRD characterization enable the examination of the phase development of alkali-activated materials at the atomic scale.