This work developed novel chitosan–halloysite nanotubes (HNTs) nanocomposite (NC) scaffolds by combining solution-mixing and freeze-drying techniques, and aimed to show the potential application of the scaffolds in tissue-engineering. The hydrogen bonding and electrostatic attraction between chitosan and HNTs were confirmed by spectroscopy and morphology analysis. The interfacial interactions resulted in a layer of chitosan absorbed on the surfaces of HNTs. The determination of mechanical and thermal properties demonstrated that the NC scaffolds exhibited significant enhancement in compressive strength, compressive modulus, and thermal stability compared with the pure chitosan scaffold. But the NC scaffolds showed reduced water uptake and increased density by the incorporation of HNTs. All the scaffolds exhibited a highly porous structure and HNTs had nearly no effect on the pore structure and porosity of the scaffolds. In order to assess cell attachment and viability on the materials, NIH3T3-E1 mouse fibroblasts were cultured on the materials. Results showed that chitosan–HNTs nanocomposites were cytocompatible even when the loading of HNTs was 80%. All these results suggested that chitosan–HNTs NC scaffolds exhibited great potential for applications in tissue engineering or as drug/gene carriers.