As 1:1 dioctahedral clay minerals, kaolinite and halloysite have similar chemical compositions. However, halloysite often possesses a nanotubular structure and special surface reactivity compared to platy kaolinite. The objective of this current work was to determine the effect of the SiO2/Al2O3 ratio on the microstructure and properties of geopolymers derived from two kinds of kaolin: platy kaolinite and nanotubular halloysite. The chemical structures and compositions of the geopolymers obtained were characterized through X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, and nuclear magnetic resonance (NMR), whereas the microstructural analysis was performed by scanning electron microscopy (SEM), the Brunauer–Emmett–Teller (BET) method, and N2 physisorption analysis. The results indicated that calcined halloysite showed greater geopolymerization reactivity than calcined kaolinite. In addition, the mechanical properties of the clay-based geopolymers depended not only on the SiO2/Al2O3 ratio but also on the morphology of the clay. Crystalline zeolite A and geopolymer were produced after alkali-activation of kaolin with a SiO2/Al2O3 ratio of 2.5; these products possessed porous and heterogeneous microstructures having poor compressive strength. As SiO2/Al2O3 ratios increased to >2.5, geopolymers with compact microstructure and high compressive strength were produced after alkali-activation of kaolin. Notably, at a given condition, halloysite-based geopolymers exhibited greater early compressive strength, more compactness, and more homogeneous microstructure than kaolinite-based geopolymers. This can be attributed to the nanotubular microstructure of halloysite, which can release more Si and Al during alkali activation than platy kaolinite. These results indicated that the various morphologies and microstructures among clays have significant impact on the microstructure and compressive strength of geopolymers.