Geopolymer has attracted attention for the process features of energy saving, reduced carbon emissions and excellent properties. In this paper, we proposed a concept of phase engineering for geopolymer, and demonstrated the utilization of calcined layered double hydroxides (CLDHs). The effects of microstructure and property in slag-based geopolymer were analyzed. The rehydration reaction and nucleation mechanism of CLDH were revealed by high-energy X-ray synchrotron radiation, pair distribution function calculation, transmission electron microscopy and other characterization techniques, thus improving the short-distance order of the gel and the crystal-to-binder ratio. For the macroscopic properties, the mechanical strength and water retention of geopolymer with CLDH are improved, and the chemical shrinkage and dry shrinkage of geopolymer are decreased. Incorporation of CLDH as a technical approach to improve the microstructure of geopolymer can remedy the performance defects of geopolymer, and is thus an effective approach for manufacturing high-performance geopolymer products.