The setting chemistry of glass ionomer cement was investigated by using mechanical determination of compressive strength at predetermined intervals, and measurement of structure changes of corresponding fracture sample by means of IR spectra and differential scanning calorimetry ( DSC). Zinc polycarboxylate cement was used as a comparison sample. The compressive strength of glass ionomer cement (GIC) increases with aging. IR spectra and DSC of corresponding fracture sample show the structure changes of the matrix and interface layer comprising of silica gel during the predetermined intervals studied, however, no significant changes occur in the zinc polycarxyolate cement. Hence the structure changes of the matrix and/or interface layer are responsible for compressive strength increasing with aging. The structure changes include the crosslink density, the ratio of complex form to ionic form, the content ratio of Al-PAA to Ca-PAA, the forming and mauring process of the interface layer comprising of silica gel.