Abstract Ordered assembly of imogolite clay nanotubes was achieved by the spatiotemporal regulation of imogolite complex formation using an organic polyelectrolyte. In a confined reaction space, imogolites formed assemblies with anisotropic birefringence and distinct optical texture under uni-directional diffusion. In assemblies with anisotropic birefringence, imogolite nanotubes uniformly aligned along the longitudinal axis of the assemblies. The ordered structure of imogolites drastically changed with the size of the reaction space and the concentration of components that control a number of nuclei in the assembly. The perfectly rigid rod-like nature of imogolite clay nanotubes induces their ordered alignment.