Fly ash was used as a raw material to immobilize the heavy metal has attracted more attention due to its availability in large quantities and its ability in improving geopolymer physical properties.The change of the microstructure of fly ash based geopolymer is still unclear.The time dependent of the band vibration of Si-O-Si and Al-O-Si in the fresh pastes of Fly ash based geopolymer were investigated using Fourier transform infrared spectroscopy in this paper.The heavy metal of Cr3+ or Cr6+ were added as constant in fresh paste of the fly ash based geopolymer.The concentrations of the heavy metal in paste were measured also, the immobilization efficiency is calculated, too.The results from immobilization efficiency of the heavy metal shown that the immobilization efficiency of Cr3+ is more than that of Cr6+ in fly ash based geopolymer.The results of FTIR indicated that the addition of Cr3+ or Cr6+ didnt influence the trend of polymerization occurred in Fly ash based geopolymer.The asymmetric stretching of Si-O-Si in the fresh paste of Fly ash based geopolymer changed.Compared with the paste without heavy metal ions, 10 cm-1 wavenumbers displacement changed while Cr6+ added within 25 min, this change stopped after 40 min;24 cm-1 wavenumbers displacement changed while Cr3+ added within 40 min.This discovery confirmed Cr3+ was easier than Cr6+ to join the Si-O-Si polymerization of the Fly ash based geopolymer.About 10 cm-1 displacement for the band of Al-O-Si occurred while Cra+ or Cr6+ incorporated, the structure of O-Si-O seems independence of Cr3+ or Cr6+ incorporation.After leaching, the Cr2p still exist in fly ash based geopolymer with Cr3+, however, the Cr2p can be seen hardly in fly ash based geopolymer with Cr6+.