Polymeric biomaterials with regular pore structure can generate distinctive properties in various biomedical applications. This study presents scaffolds comprising chitin, chitosan, and gelatin with pore geometry of inverted colloidal crystals (ICC) for guiding differentiation of induced pluripotent stem (iPS) cells toward neurons. Chitin–chitosan–gelatin ICC scaffolds were fabricated by self-assembly, crosslinking, infiltration, dehydration, and particle leaching. The results revealed that ethanol as a dispersion medium yielded a higher regularity of colloidal template than ethylene glycol. For the adhesion of iPS cells, freeform constructs were more efficient than ICC constructs. The reverse was true for the viability of iPS cells. The quantity of stage-specific embryonic surface antigen-1 in cultured freeform construct was larger than that in cultured ICC construct, indicating that the former preserved more phenotypic characteristics of iPS cells than the latter. Moreover, β III tubulin-identified region in ICC construct was larger than that in freeform construct, demonstrating that the differentiation of iPS cells toward neurons in ICC construct was faster than that in freeform construct. ICC topography in chitin–chitosan–gelatin scaffolds can accelerate neuronal differentiation of iPS cells.