Hexagonal hierarchical microtubular structures are produced by diphenylalanine self-assembly and the ratio of the relative humidity in the growth chamber to the diphenylalanine concentration (defined as the RH-FF ratio) determines the microtubular morphology. The hexagonal arrangement of the diphenylalanine molecules first induces the hexagonal nanotubes with opposite charges on the two ends, and the dipolar electric field on the nanotubes serves as the driving force. Side-by-side hexagonal aggregation and end-to-end arrangement ensue finally producing a hexagonal hierarchical microtubular structure. Staining experiments and the external electric field-induced parallel arrangement provide evidence of the existence of opposite charges and dipolar electric field. In this self-assembly, the different RH-FF ratios induce different contents of crystalline phases. This leads to different initial nanotube numbers finally yielding different microtubular morphologies. Our calculation based on the dipole model supports the dipole-field mechanism that leads to the different microtubular morphologies.