Halloysite structure is often considered as kaolinite's structure, however, halloysite mostly presents a spiral tubular morphology instead of platy. Several probable reasons were described for such differentiation, but still without a clear explanation. A new structural point of view for the explanation of halloysite's morphology is proposed in this study and supported by Fourier-Transform Infrared Spectroscopy, X-ray Diffraction, Transmission Electron Microscopy, Scanning Electron Microscopy and, Thermogravimetric Analysis in combination with Molecular Dynamics and Density Functional Theory calculations. Based on the present calculations, the two-two type structure, that means the distance between two Si tetrahedra in one sheet is undertaken by two oxygen atoms bonded to different Al octahedra, is preferred for the rolling mechanism of halloysite with respect to two-one structure, where distance of the neighboring Si tetrahedra in one sheet is undertaken by two oxygen atoms bonded to one Al octahedra in the octahedral sheet. A completely new program “Nanotube generator” was created for the generation of various structural models from platy, cylindrical to spiral shape structures as halloysite presents. The software is based on mathematical or real physical quantities that are derived from experimental measurements.