Hollow glass microspheres (HGMs)/epoxy syntactic foam were reinforced by hybrid functionalized carbon nanotubes that were synthesized by simultaneous covalent and noncovalent functionalization of carbon nanotubes. The effect of hybrid functionalized carbon nanotubes on density, mechanical properties, and water absorption of HGMs/epoxy syntactic foam was studied. The study indicated that the dispersion of carbon nanotubes in epoxy resin can be improved by hybrid functionalization. The compression strength of syntactic foam reinforced by hybrid functionalized carbon nanotubes was significantly enhanced. The maximum compressive strength of syntactic foam corresponding to chitosan modified carbon nanotubes approached 60 MPa. Hybrid functionalized carbon nanotubes had little effect on the water absorption ability of syntactic foam, and was less than 1%.